Diversity report for diversity outbred mice

After finishing 06_final_pr_apr_69K.R, 07_do_diversity_report.R, all the output will be used plot DO Diversity Report for 12 batches of DO mice

library

# Load packages
library(qtl2)
library(table1)
library(tidyverse)
library(data.table)
library(foreach)
library(doParallel)
library(parallel)
library(abind)
library(gap)
library(regress)
library(lme4)
library(abind)
library(ggplot2)
library(vcd)
library(MASS)
#library(plotly)
library(colorspace)
library(HardyWeinberg)

Warning: package 'HardyWeinberg' was built under R version 4.0.4

options(stringsAsFactors = FALSE)
source("code/reconst_utils.R")

#Summary

load("data/Jackson_Lab_12_batches/gm_DO3173_qc.RData")#gm_after_qc

# make dataset with a few variables to summarize
table1 <- gm_after_qc$covar %>% 
  dplyr::select(Name = name, 
                Sex  = sex, 
                Generation = ngen) %>%
  mutate(Sex = case_when(
    Sex == "F" ~ "Female",
    Sex == "M" ~ "Male"
  ))

# summarize the data 
table1(~ Generation | Sex, data=table1)

#Founder contributions

load("data/Jackson_Lab_12_batches/fp_DO3173.RData") #fp and fp_summary object
#change order of level in gen
fp$gen <- factor(fp$gen,levels = c(21,22,23,25,29,30,31,32,33,34,35,36))

#summarize per generation per chromosome
fp_summary = fp %>% group_by(chr, founder, gen) %>%
  summarize(mean = round(100*mean(prop), 2),
            sd   = round(100*sd(prop), 2))

`summarise()` regrouping output by 'chr', 'founder' (override with `.groups` argument)

#Stackbar plot
#summarize per chromosome across generation
pdf(file = "data/Jackson_Lab_12_batches/stackbar_mean_prop_across_all_gen.pdf",width = 16)
p01 <- fp %>% group_by(chr, founder) %>%
  summarise(grand_mean = round(100*mean(prop), 2)) %>%
  ggplot(aes(x = chr, y = grand_mean, fill = founder)) +
    geom_bar(stat="identity",
             width=1) +
    geom_text(aes(label = paste0(grand_mean)), position = position_stack(vjust = 0.5)) +
    scale_fill_manual(values = CCcolors) +
    ylab("Mean percentage across generations") +
    xlab("Chromosome") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.line = element_line(colour = "black"),
          plot.title = element_text(hjust = 0.5),
          text = element_text(size=16),
          axis.title=element_text(size=16),
          legend.title=element_blank())

`summarise()` regrouping output by 'chr' (override with `.groups` argument)

p01
dev.off()

png 
  2 

p01

Past versions of “Founder contributions-1.png”

#Stackbar plot
#summarize per chromosome across generation
pdf(file = "data/Jackson_Lab_12_batches/stackbar_mean_prop_across_all_chr.pdf",width = 16)
p02 <- fp %>% group_by(gen, founder) %>%
  summarise(grand_mean = round(100*mean(prop), 2), 
            grand_sd   = round(100*sd(prop), 2)) %>%
  ggplot(aes(x = gen, y = grand_mean, fill = founder)) +
    geom_bar(stat="identity",
             width=0.99) +
    geom_text(aes(label = paste0(grand_mean, " ± ", grand_sd)), position = position_stack(vjust = 0.5)) +
    scale_fill_manual(values = CCcolors) +
    ylab("Mean percentage across all chromosomes") +
    xlab("Generation") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.line = element_line(colour = "black"),
          plot.title = element_text(hjust = 0.5),
          text = element_text(size=16),
          axis.title=element_text(size=16),
          legend.title=element_blank())

`summarise()` regrouping output by 'gen' (override with `.groups` argument)

p02
dev.off()

png 
  2 

p02

Past versions of “Founder contributions-2.png”

#stackbar_prop_across_gen
for(c in c(1:19, "X")){
  #print(c)
  p <- ggplot(data = fp_summary[fp_summary$chr == c,], aes(x = gen, y = mean, fill = founder)) +
    geom_bar(stat="identity",
             width=1) +
    geom_text(aes(label = paste0(mean," ± ", sd)), position = position_stack(vjust = 0.5)) +
    scale_fill_manual(values = CCcolors) +
    labs(title = paste0("Chr ", c)) +
    ylab("Percentage") +
    xlab("Generation") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.line = element_line(colour = "black"),
          plot.title = element_text(hjust = 0.5),
          text = element_text(size=16),
          axis.title=element_text(size=16),
          legend.title=element_blank())
  print(p)
}

Past versions of “Founder contributions-3.png”

Past versions of “Founder contributions-4.png”

Past versions of “Founder contributions-5.png”

Past versions of “Founder contributions-6.png”

Past versions of “Founder contributions-7.png”

Past versions of “Founder contributions-8.png”

Past versions of “Founder contributions-9.png”

Past versions of “Founder contributions-10.png”

Past versions of “Founder contributions-11.png”

Past versions of “Founder contributions-12.png”

Past versions of “Founder contributions-13.png”

Past versions of “Founder contributions-14.png”

Past versions of “Founder contributions-15.png”

Past versions of “Founder contributions-16.png”

Past versions of “Founder contributions-17.png”

Past versions of “Founder contributions-18.png”

Past versions of “Founder contributions-19.png”

Past versions of “Founder contributions-20.png”

Past versions of “Founder contributions-21.png”

Past versions of “Founder contributions-22.png”

pdf(file = "data/Jackson_Lab_12_batches/stackbar_prop_across_gen.pdf",width = 16)
for(c in c(1:19, "X")){
  #print(c)
  p <- ggplot(data = fp_summary[fp_summary$chr == c,], aes(x = gen, y = mean, fill = founder)) +
    geom_bar(stat="identity",
             width=1) +
    geom_text(aes(label = paste0(mean," ± ", sd)), position = position_stack(vjust = 0.5)) +
    scale_fill_manual(values = CCcolors) +
    labs(title = paste0("Chr ", c)) +
    ylab("Percentage") +
    xlab("Generation") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.line = element_line(colour = "black"),
          plot.title = element_text(hjust = 0.5),
          text = element_text(size=16),
          axis.title=element_text(size=16),
          legend.title=element_blank())
  print(p)
}
dev.off()

png 
  2 

#stackbar_prop_across_chr
for(g in levels(fp_summary$gen)){
  #print(g)
  p <- ggplot(data = fp_summary[fp_summary$gen == g,], aes(x = chr, y = mean, fill = founder)) +
    geom_bar(stat="identity",
             width=1) +
    geom_text(aes(label = paste0(mean)), position = position_stack(vjust = 0.5)) +
    scale_fill_manual(values = CCcolors) +
    labs(title = paste0("Generation ", g)) +
    ylab("Percentage") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.title.x = element_blank(),
          axis.line = element_line(colour = "black"),
          plot.title = element_text(hjust = 0.5),
          text = element_text(size=16),
          axis.title=element_text(size=16),
          legend.title=element_blank())
  #print(p)
}

pdf(file = "data/Jackson_Lab_12_batches/stackbar_prop_across_chr.pdf", width = 12)
for(g in levels(fp_summary$gen)){
  #print(g)
  p <- ggplot(data = fp_summary[fp_summary$gen == g,], aes(x = chr, y = mean, fill = founder)) +
    geom_bar(stat="identity",
             width=1) +
    geom_text(aes(label = paste0(mean)), position = position_stack(vjust = 0.5)) +
    scale_fill_manual(values = CCcolors) +
    labs(title = paste0("Generation ", g)) +
    ylab("Percentage") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.title.x = element_blank(),
          axis.line = element_line(colour = "black"),
          plot.title = element_text(hjust = 0.5),
          text = element_text(size=16),
          axis.title=element_text(size=16),
          legend.title=element_blank())
  print(p)
}
dev.off()

png 
  2 

#line plot
#plt <- htmltools::tagList()
for(c in unique(names(gm_after_qc$geno))){
  print(c)
  fp_subdata <- fp[fp$chr == c,]
  pp <- ggplot(data = fp_subdata,aes(pos, prop, group = gen, color = founder)) +
    geom_line(aes(linetype=gen)) +
    scale_linetype_manual(values=rep("solid",12)) +
    geom_hline(yintercept=0.125, linetype="dashed", color = "black", size = 0.25) +
    scale_color_manual(values = CCcolors) +
    facet_grid(founder~.) + 
    labs(title = paste0("Chr ", c)) + 
    theme(legend.position='none')
  print(pp)
  # Print an interactive plot
  # Add to list
  #plt[[c]] <- as_widget(ggplotly(pp, width = 1000, height = 1000))
}

[1] "1"

Past versions of “Founder contributions-23.png”

[1] "2"

Past versions of “Founder contributions-24.png”

[1] "3"

Past versions of “Founder contributions-25.png”

[1] "4"

Past versions of “Founder contributions-26.png”

[1] "5"

Past versions of “Founder contributions-27.png”

[1] "6"

Past versions of “Founder contributions-28.png”

[1] "7"

Past versions of “Founder contributions-29.png”

[1] "8"

Past versions of “Founder contributions-30.png”

[1] "9"

Past versions of “Founder contributions-31.png”

[1] "10"

Past versions of “Founder contributions-32.png”

[1] "11"

Past versions of “Founder contributions-33.png”

[1] "12"

Past versions of “Founder contributions-34.png”

[1] "13"

Past versions of “Founder contributions-35.png”

[1] "14"

Past versions of “Founder contributions-36.png”

[1] "15"

Past versions of “Founder contributions-37.png”

[1] "16"

Past versions of “Founder contributions-38.png”

[1] "17"

Past versions of “Founder contributions-39.png”

[1] "18"

Past versions of “Founder contributions-40.png”

[1] "19"

Past versions of “Founder contributions-41.png”

[1] "X"

Past versions of “Founder contributions-42.png”

#plt

#Average haplotype block size

load("data/Jackson_Lab_12_batches/recom_block_size.RData")
#Create an appropriately sized vector of names
nameVector <- unlist(mapply(function(x,y){ rep(y, length(x)) }, pos_ind_gen, names(pos_ind_gen)))
#Create the result
recom_block <- cbind.data.frame(unlist(pos_ind_gen), nameVector)
colnames(recom_block) <- c("sizeblock",
                           "ngen")
#remove 0
recom_block <- recom_block[recom_block$sizeblock != 0,]
recom_block$ngen <- factor(recom_block$ngen, levels = as.character(c(21:36)))
#mean
means <- aggregate(sizeblock~ngen, data= recom_block,mean)
means$sizeblock <- round(means$sizeblock, 2)

pdf(file = "data/Jackson_Lab_12_batches/boxplot_mean_recomb_block_size.pdf", height = 8, width = 10)
p1 <- ggplot(recom_block, aes(x=ngen, y=sizeblock, group = ngen, fill = ngen)) + 
  geom_boxplot(show.legend = F , outlier.size = 0.5, notchwidth = 3) +
  scale_x_discrete(drop=FALSE, breaks = c(21:23,NA,25,rep(NA,3),29:36)) +
  scale_fill_discrete_qualitative(palette = "warm")+
  geom_text(data = means, alpha = 0.85, aes(label = sizeblock, y = sizeblock + 0.15 )) + 
  ylab("Recombination Block Size (Mb)") +
  xlab("Generation") +
  labs(fill = "") +
  #ylim(c(0, 60)) +
  scale_y_continuous(breaks=c(0,5,10, 20, 40, 60), limits=c(0, 60)) +
  theme(panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank(),
        panel.background = element_blank(), 
        axis.line = element_line(colour = "black"),
        text = element_text(size=16), 
        axis.title=element_text(size=16)) +
  guides(shape = guide_legend(override.aes = list(size = 12)))
p1
dev.off()

png 
  2 

p1

Past versions of “Average haplotype block size-1.png”

#block size distribution
for(g in unique(gm_after_qc$covar$ngen)){
  #plot for recom block size
  #png(paste0("data/Jackson_Lab_12_batches/DO_recom_block_size_G", g, ".png"))
  x <- pos_ind_gen[[g]][pos_ind_gen[[g]] != 0]
  # estimate the parameters
  fit1 <- fitdistr(x, "exponential") 
  
  # goodness of fit test
  ks.test(x, "pexp", fit1$estimate) # p-value > 0.05 -> distribution not refused
  
  # plot a graph
  hist(x, 
       freq = FALSE, 
       breaks = 200, 
       xlim = c(0, 5+quantile(x, 1)), 
       #ylim = c(0,0.3),
       xlab = "Recombination Block Size (Mb)", 
       main = paste0("Gen ", g))
  curve(dexp(x, rate = fit1$estimate), 
        from = 0, 
        to = 5+quantile(x, 1), 
        col = "red", 
        add = TRUE)
  #dev.off()
}

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-2.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-3.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-4.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-5.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-6.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-7.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-8.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-9.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-10.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-11.png”

Warning in ks.test(x, "pexp", fit1$estimate): ties should not be present for the
Kolmogorov-Smirnov test

Past versions of “Average haplotype block size-12.png”

Past versions of “Average haplotype block size-13.png”

#Average heterozygosity value

load("data/Jackson_Lab_12_batches/dat_het_ind_pr.RData")
dat_het_ind_pr$ngen <- factor(dat_het_ind_pr$ngen, levels = as.character(c(21:36)))

pdf(paste("data/Jackson_Lab_12_batches/DO_Heterozygosity_value_violin_genoprops.pdf"), width = 10, height =8)
p2 <- ggplot(dat_het_ind_pr, aes(x=ngen, y=het, group=ngen, fill=ngen)) +
  geom_violin(show.legend = FALSE) +
  geom_boxplot(show.legend = FALSE, width=0.35, color="black", alpha=0.6) +
  scale_x_discrete(drop=FALSE, breaks = c(21:23,NA,25,rep(NA,3),29:36)) +
  scale_fill_discrete_qualitative(palette = "warm")+
  ylab("Heterozygosity from genotype props") +
  xlab("Generation") +
  ylim(c(0.65, 1)) +
  geom_hline(yintercept=0.875, linetype="dashed", color = "red") +
  #scale_y_continuous(breaks=c(0.55, 0.65, 0.75, 0.85, 0.95, 1), limits=c(0.55, 1)) +
  theme(panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.background = element_blank(),
        axis.line = element_line(colour = "black"),
        text = element_text(size=16),
        axis.title=element_text(size=16),
        legend.title=element_blank())
p2
dev.off()

png 
  2 

p2

Past versions of “Average heterozygosity value-1.png”

#marker UNC13316610 allele frequency

T_freq <- unique(gm_after_qc$covar$ngen) %>%
  map(~(read.table(paste0("data/GCTA/12_batches_QC_id_gen", .x,".frq"), header = TRUE) %>%
          filter(SNP == "UNC13316610") %>%
          mutate(GEN = .x, .before = 1))
        ) %>%
  set_names(., nm = unique(gm_after_qc$covar$ngen)) %>%
  bind_rows() %>%
  mutate(allele = "T",
         MAF_allele = case_when(
           A1 == "T" ~ MAF,
           A1 != "T" ~ 1-MAF
         ))
C_freq <- T_freq %>%
  mutate(allele = "C",
         MAF_allele = 1-MAF_allele
         )
#bind
UNC13316610.freq <- bind_rows(T_freq, C_freq)
# Stacked
p <- ggplot(UNC13316610.freq, aes(fill=allele, y=MAF_allele, x=GEN)) + 
  geom_bar(position="stack", stat="identity") +
  scale_fill_manual(values=c("#3399CC", "#FFCC33")) +
  xlab("Generation") +
  ylab("UNC13316610 allele frequency")
print(p)

#pull marker UNC13316610
gm.UNC13316610 <- pull_markers(gm_after_qc, "UNC13316610")
#genotype freq
gfreq <- calc_raw_geno_freq(gm.UNC13316610)
gfreq_tab <- gfreq %>%
  as.data.frame() %>%
  mutate(id = rownames(gfreq)) %>%
  left_join(gm_after_qc$covar) %>%
  group_by(ngen)

Joining, by = "id"

#gfreq_tab
tab <- gfreq_tab %>%
  group_map(~(apply(.x[,1:3],2,function(x)(sum(x,na.rm = T))))) %>%
  bind_rows() %>%
  mutate(Genertation = group_keys(gfreq_tab)$ngen, .before = 1) %>%
  left_join(C_freq[,c("GEN", "MAF_allele")], by = c("Genertation" = "GEN")) %>%
  left_join(T_freq[,c("GEN", "MAF_allele")], by = c("Genertation" = "GEN")) %>%
  rename(C_freq = MAF_allele.x) %>%
  rename(T_freq = MAF_allele.y) %>%
  mutate(C_freq2 = (2*AA + AB)/(2*(AA+AB+BB))) %>%
  rowwise() %>%
  mutate(chisq = HWChisq(c(AA, AB, BB))$chisq,
         df    = HWChisq(c(AA, AB, BB))$df,
         p     = HWChisq(c(AA, AB, BB))$p) %>%
  dplyr::select(Genertation = Genertation,
                CC = AA,
                CT = AB,
                TT = BB,
                C_freq,
                T_freq,
                chisq,
                p)

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 1.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 1.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  3.64016 DF =  1 p-value =  0.05640151 D =  -6.027027 f =  0.1672918 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 2.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 2.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.0139537 DF =  1 p-value =  0.905968 D =  -0.03870968 f =  0.001017639 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 3.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 3.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.5915421 DF =  1 p-value =  0.4418234 D =  -3.003886 f =  0.06323453 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 4.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 4.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1041667 DF =  1 p-value =  0.7468856 D =  0 f =  0 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 5.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 5.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  2.206823 DF =  1 p-value =  0.1374014 D =  7.037121 f =  -0.08638439 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 6.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 6.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.07948221 DF =  1 p-value =  0.7780003 D =  1.835812 f =  -0.01689436 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 7.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 7.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.01635285 DF =  1 p-value =  0.8982453 D =  1.014388 f =  -0.009755085 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 8.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 8.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.582596 DF =  1 p-value =  0.4452966 D =  -3.727918 f =  0.04765457 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 9.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 9.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.250779 DF =  1 p-value =  0.6165271 D =  3.027222 f =  -0.02691515 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 10.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 10.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  2.441985 DF =  1 p-value =  0.1181267 D =  8.184275 f =  -0.08118054 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 11.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 11.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  1.695457 DF =  1 p-value =  0.1928832 D =  4.53811 f =  -0.1107886 

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 12.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `chisq`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `chisq` is `HWChisq(c(AA, AB, BB))$chisq`.
ℹ The error occurred in row 12.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1576923 DF =  1 p-value =  0.6912901 D =  -1.5 f =  0.04615385 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 1.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 1.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  3.64016 DF =  1 p-value =  0.05640151 D =  -6.027027 f =  0.1672918 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 2.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 2.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.0139537 DF =  1 p-value =  0.905968 D =  -0.03870968 f =  0.001017639 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 3.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 3.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.5915421 DF =  1 p-value =  0.4418234 D =  -3.003886 f =  0.06323453 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 4.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 4.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1041667 DF =  1 p-value =  0.7468856 D =  0 f =  0 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 5.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 5.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  2.206823 DF =  1 p-value =  0.1374014 D =  7.037121 f =  -0.08638439 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 6.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 6.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.07948221 DF =  1 p-value =  0.7780003 D =  1.835812 f =  -0.01689436 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 7.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 7.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.01635285 DF =  1 p-value =  0.8982453 D =  1.014388 f =  -0.009755085 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 8.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 8.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.582596 DF =  1 p-value =  0.4452966 D =  -3.727918 f =  0.04765457 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 9.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 9.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.250779 DF =  1 p-value =  0.6165271 D =  3.027222 f =  -0.02691515 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 10.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 10.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  2.441985 DF =  1 p-value =  0.1181267 D =  8.184275 f =  -0.08118054 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 11.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 11.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  1.695457 DF =  1 p-value =  0.1928832 D =  4.53811 f =  -0.1107886 

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 12.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `df`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `df` is `HWChisq(c(AA, AB, BB))$df`.
ℹ The error occurred in row 12.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1576923 DF =  1 p-value =  0.6912901 D =  -1.5 f =  0.04615385 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 1.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 1.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  3.64016 DF =  1 p-value =  0.05640151 D =  -6.027027 f =  0.1672918 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 2.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 2.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.0139537 DF =  1 p-value =  0.905968 D =  -0.03870968 f =  0.001017639 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 3.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 3.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.5915421 DF =  1 p-value =  0.4418234 D =  -3.003886 f =  0.06323453 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 4.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 4.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1041667 DF =  1 p-value =  0.7468856 D =  0 f =  0 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 5.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 5.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  2.206823 DF =  1 p-value =  0.1374014 D =  7.037121 f =  -0.08638439 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 6.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 6.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.07948221 DF =  1 p-value =  0.7780003 D =  1.835812 f =  -0.01689436 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 7.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 7.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.01635285 DF =  1 p-value =  0.8982453 D =  1.014388 f =  -0.009755085 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 8.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 8.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.582596 DF =  1 p-value =  0.4452966 D =  -3.727918 f =  0.04765457 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 9.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 9.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.250779 DF =  1 p-value =  0.6165271 D =  3.027222 f =  -0.02691515 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 10.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 10.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  2.441985 DF =  1 p-value =  0.1181267 D =  8.184275 f =  -0.08118054 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 11.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 11.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  1.695457 DF =  1 p-value =  0.1928832 D =  4.53811 f =  -0.1107886 

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels (AA, AB, BB) assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 12.

Warning in homozyg(X): Genotypes are not labelled, default labels (AA, AB, BB)
assumed.

Warning: Problem with `mutate()` input `p`.
ℹ Genotypes are not labelled, default labels assumed.
ℹ Input `p` is `HWChisq(c(AA, AB, BB))$p`.
ℹ The error occurred in row 12.

Warning in heterozyg(X): Genotypes are not labelled, default labels assumed.

Chi-square test with continuity correction for Hardy-Weinberg equilibrium (autosomal)
Chi2 =  0.1576923 DF =  1 p-value =  0.6912901 D =  -1.5 f =  0.04615385 

tab

# A tibble: 12 x 8
# Rowwise: 
   Genertation    CC    CT    TT C_freq T_freq  chisq     p
   <chr>       <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl> <dbl>
 1 21             56    60    32  0.581  0.419 3.64   0.419
 2 22             50    76    29  0.562  0.438 0.0140 0.432
 3 23             64    89    40  0.562  0.438 0.592  0.438
 4 25              6    12     6  0.5    0.5   0.104  0.5  
 5 29             95   177    58  0.556  0.444 2.21   0.444
 6 30            124   221    92  0.537  0.463 0.0795 0.463
 7 31            114   210    93  0.525  0.475 0.0164 0.475
 8 32            102   149    66  0.557  0.443 0.583  0.443
 9 33            113   231   106  0.508  0.492 0.251  0.492
10 34             75   218   114  0.452  0.548 2.44   0.452
11 35             34    91    39  0.485  0.515 1.70   0.485
12 36             34    62    34  0.5    0.5   0.158  0.5  

Session information

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DOQTL_1.0.0         HardyWeinberg_1.7.2 Rsolnp_1.16        
 [4] mice_3.12.0         colorspace_2.0-0    MASS_7.3-53        
 [7] vcd_1.4-8           lme4_1.1-26         Matrix_1.2-18      
[10] regress_1.3-21      gap_1.2.2           abind_1.4-5        
[13] doParallel_1.0.16   iterators_1.0.13    foreach_1.5.1      
[16] data.table_1.13.6   forcats_0.5.0       stringr_1.4.0      
[19] dplyr_1.0.2         purrr_0.3.4         readr_1.4.0        
[22] tidyr_1.1.2         tibble_3.0.4        ggplot2_3.3.2      
[25] tidyverse_1.3.0     table1_1.2.1        qtl2_0.24          
[28] workflowr_1.6.2    

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           MUGAExampleData_1.10.0 backports_1.2.0       
  [4] BiocFileCache_1.14.0   splines_4.0.3          BiocParallel_1.22.0   
  [7] GenomeInfoDb_1.26.2    digest_0.6.27          htmltools_0.5.0       
 [10] gdata_2.18.0           fansi_0.4.1            magrittr_2.0.1        
 [13] memoise_1.1.0          QTLRel_1.6             Biostrings_2.58.0     
 [16] annotate_1.66.0        modelr_0.1.8           askpass_1.1           
 [19] prettyunits_1.1.1      blob_1.2.1             rvest_0.3.6           
 [22] rappdirs_0.3.1         haven_2.3.1            xfun_0.19             
 [25] crayon_1.3.4           RCurl_1.98-1.2         jsonlite_1.7.1        
 [28] org.Mm.eg.db_3.11.4    zoo_1.8-8              glue_1.4.2            
 [31] gtable_0.3.0           zlibbioc_1.36.0        XVector_0.30.0        
 [34] BiocGenerics_0.36.0    scales_1.1.1           DBI_1.1.0             
 [37] Rcpp_1.0.5             xtable_1.8-4           progress_1.2.2        
 [40] mclust_5.4.7           bit_4.0.4              Formula_1.2-4         
 [43] stats4_4.0.3           truncnorm_1.0-8        httr_1.4.2            
 [46] ellipsis_0.3.1         farver_2.0.3           pkgconfig_2.0.3       
 [49] XML_3.99-0.5           dbplyr_2.0.0           utf8_1.1.4            
 [52] labeling_0.4.2         tidyselect_1.1.0       rlang_0.4.9           
 [55] later_1.1.0.1          AnnotationDbi_1.52.0   munsell_0.5.0         
 [58] cellranger_1.1.0       tools_4.0.3            cli_2.2.0             
 [61] generics_0.1.0         RSQLite_2.2.2          broom_0.7.2           
 [64] evaluate_0.14          yaml_2.2.1             org.Hs.eg.db_3.11.4   
 [67] knitr_1.30             bit64_4.0.5            fs_1.5.0              
 [70] nlme_3.1-149           whisker_0.4            xml2_1.3.2            
 [73] biomaRt_2.44.4         compiler_4.0.3         rstudioapi_0.13       
 [76] curl_4.3               reprex_0.3.0           statmod_1.4.35        
 [79] stringi_1.5.3          ps_1.5.0               annotationTools_1.64.0
 [82] lattice_0.20-41        nloptr_1.2.2.2         vctrs_0.3.5           
 [85] pillar_1.4.7           lifecycle_0.2.0        RUnit_0.4.32          
 [88] lmtest_0.9-38          bitops_1.0-6           corpcor_1.6.9         
 [91] httpuv_1.5.5           GenomicRanges_1.42.0   R6_2.5.0              
 [94] hwriter_1.3.2          promises_1.1.1         IRanges_2.24.1        
 [97] codetools_0.2-16       boot_1.3-25            gtools_3.8.2          
[100] assertthat_0.2.1       openssl_1.4.3          rprojroot_2.0.2       
[103] withr_2.3.0            Rsamtools_2.4.0        S4Vectors_0.28.1      
[106] GenomeInfoDbData_1.2.4 hms_0.5.3              minqa_1.2.4           
[109] rmarkdown_2.5          git2r_0.28.0           Biobase_2.50.0        
[112] lubridate_1.7.9.2