Last updated: 2019-08-01

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Knit directory: apaQTL/analysis/

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File Version Author Date Message
Rmd 1ef5cad brimittleman 2019-08-01 figure2b2c
html c5bf3fd brimittleman 2019-07-02 Build site.
Rmd 36d86c0 brimittleman 2019-07-02 post LM plot midifications
html 62ab1cc brimittleman 2019-06-21 Build site.
Rmd f0e8ce1 brimittleman 2019-06-21 merge fracs
html c0a090f brimittleman 2019-06-21 Build site.
html 4912eaa brimittleman 2019-06-14 Build site.
Rmd bf91cb3 brimittleman 2019-06-14 add location plot

In this analysis I want to look at the location of the apaQTLs first looking at distance to PAS. Until now I have been using the distance to the peak and have not flipped the strand. This showed me QTLs are close to the PAS but was not the most correct way to do this.

library(workflowr)
This is workflowr version 1.4.0
Run ?workflowr for help getting started
library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
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library(cowplot)

Attaching package: 'cowplot'
The following object is masked from 'package:ggplot2':

    ggsave
PAS=read.table("../data/PAS/APAPAS_GeneLocAnno.5perc.bed",col.names = c("chr", "start", "PASloc", "name", "score", "strand"), stringsAsFactors = F )%>% separate(name, into=c("peakNum", "geneloc"), sep=":") %>% mutate(peak=paste("peak", peakNum, sep="")) %>% select(PASloc, peak)

Distance to PAS

Total:

totQTLs=read.table("../data/apaQTLs/Total_apaQTLs4pc_5fdr.WITHSTRAND.bed",stringsAsFactors = F, header=T)%>%
  separate(name, into=c("gene", "peak", "loc"), sep=":") %>% 
  inner_join(PAS, by="peak") %>% 
  mutate(distance=SNPend-PASloc, dist2PAS=ifelse(strand=="-", -1 *distance, distance))
ggplot(totQTLs, aes(x=dist2PAS, by=loc, fill=loc)) + geom_histogram(bins=100) 

Version Author Date
4912eaa brimittleman 2019-06-14

Plot by proportion:

ggplot(totQTLs, aes(x=dist2PAS, fill=loc)) + geom_histogram( bins=100) + facet_grid(~loc)

Version Author Date
4912eaa brimittleman 2019-06-14

Nuclear

nucQTLs=read.table("../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.WITHSTRAND.bed",stringsAsFactors = F, header=T)%>%
  separate(name, into=c("gene", "peak", "loc"), sep=":") %>% 
  inner_join(PAS, by="peak") %>% 
  mutate(distance=SNPend-PASloc, dist2PAS=ifelse(strand=="-", -1 *distance, distance))
ggplot(nucQTLs, aes(x=dist2PAS, by=loc, fill=loc)) + geom_histogram(bins=100)

Version Author Date
4912eaa brimittleman 2019-06-14
ggplot(nucQTLs, aes(x=dist2PAS, fill=loc)) + geom_histogram( bins=100) + facet_grid(~loc)

Version Author Date
4912eaa brimittleman 2019-06-14

Plot total and nuclear together:

totalQTLdist=totQTLs %>% select(dist2PAS) %>% mutate(Fraction="Total")
nuclearQTLdist=nucQTLs %>% select(dist2PAS) %>% mutate(Fraction="Nuclear")
bothFractDist=bind_rows(totalQTLdist, nuclearQTLdist)

PASdistplot=ggplot(bothFractDist, aes(x=dist2PAS, fill=Fraction )) + geom_histogram(bins=100,aes(y = (..count..)/sum(..count..))) +labs(y="Proportion of apaQTLs", x="Distance QTL SNP to PAS", title="Distance from QTL SNP to PAS by Fraction") + scale_fill_manual(values=c("deepskyblue3","darkviolet"))  + facet_grid(~Fraction) + theme(text = element_text(size=16),legend.position = "bottom", axis.text.x =element_text(size=14), axis.text.y=element_text(size=14))
ggplot(bothFractDist, aes(x=dist2PAS, fill=Fraction )) + geom_density() +labs( x="Distance QTL SNP to PAS", title="Distance from QTL SNP to PAS") + scale_fill_manual(values=c("deepskyblue3","darkviolet")) + facet_grid(~Fraction) + theme(legend.position = "none")

Metagene plot

I want to plot by normalized position in the gene.

genes=read.table("../../genome_anotation_data/refseq.ProteinCoding.bed",col.names = c("chrom", "Genestart", "Geneend", "gene", "score", "strand") ,stringsAsFactors = F) %>% select(Genestart, Geneend, gene)

Total:

totQTLs_gene= totQTLs %>% inner_join(genes, by="gene")%>% mutate(geneLength=Geneend-Genestart) %>% mutate(dist2QTL=ifelse(strand=="+",as.numeric(SNPend)-as.numeric(Genestart), as.numeric(Geneend)-as.numeric(SNPend)), propGene=dist2QTL/geneLength)  %>% filter(propGene>-3 & propGene<3)
ggplot(totQTLs_gene, aes(x=propGene, fill=loc)) + geom_histogram(bins=50)  + labs(x="Proportion of gene body", y="number QTLs", title="Total apaQTLs") + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")

Version Author Date
c5bf3fd brimittleman 2019-07-02
62ab1cc brimittleman 2019-06-21
totQTLs_gene_intron_utr= totQTLs_gene %>% filter(loc=="intron"| loc =="utr3")
ggplot(totQTLs_gene_intron_utr, aes(x=propGene, fill=loc)) + geom_density()  + labs(x="Proportion of gene body", title="Total apaQTLs") + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")

Version Author Date
c5bf3fd brimittleman 2019-07-02
4912eaa brimittleman 2019-06-14

There are about 48 QTLs outside.

I can look at only those in the gene body:

totQTLs_gene_body= totQTLs_gene %>% filter(propGene>=0, propGene<=1)
  
ggplot(totQTLs_gene_body, aes(x=propGene, fill=loc)) + geom_histogram(bins=50)  + labs(x="Proportion of gene body", y="number QTLs", title="Total apaQTLs in gene body") 

Version Author Date
62ab1cc brimittleman 2019-06-21
4912eaa brimittleman 2019-06-14

There are 181 in the gene body

Nuclear:

nucQTLs_gene= nucQTLs %>% inner_join(genes, by="gene")%>% mutate(geneLength=Geneend-Genestart)%>% mutate(dist2QTL=ifelse(strand=="+",as.numeric(SNPend)-as.numeric(Genestart), as.numeric(Geneend)-as.numeric(SNPend)), propGene=dist2QTL/geneLength)  %>% filter(propGene>-3 & propGene<3)
ggplot(nucQTLs_gene, aes(x=propGene, fill=loc)) + geom_histogram(bins=50)  + labs(x="Proportion of gene body", y="number QTLs", title="Nuclear apaQTLs") + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")

Version Author Date
c5bf3fd brimittleman 2019-07-02
62ab1cc brimittleman 2019-06-21
nucQTLs_gene_intron_utr= nucQTLs_gene %>% filter(loc=="intron"| loc =="utr3")
ggplot(nucQTLs_gene_intron_utr, aes(x=propGene, fill=loc)) + geom_density()  + labs(x="Proportion of gene body", title="Nuclear apaQTLs") + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")

Version Author Date
c5bf3fd brimittleman 2019-07-02
62ab1cc brimittleman 2019-06-21

there are 77 outside of 500% of gene body

nucQTLs_gene_body= nucQTLs_gene %>% filter(propGene>=0, propGene<=1)

ggplot(nucQTLs_gene_body, aes(x=propGene, fill=loc)) + geom_histogram(bins=50)  + labs(x="Proportion of gene body", y="number QTLs", title="Nuclear apaQTLs in gene body") 

Version Author Date
c5bf3fd brimittleman 2019-07-02

334 are in the gene body.

Plot both togther:

nucQTLs_geneprop= nucQTLs_gene %>% select(propGene) %>% mutate(Fraction="Nuclear")
totQTLs_geneprop= totQTLs_gene %>% select(propGene) %>% mutate(Fraction="Total")
genepropboth=bind_rows(totQTLs_geneprop,nucQTLs_geneprop)

ggplot(genepropboth, aes(x=propGene,fill=Fraction)) + geom_histogram(bins=100) + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")+ scale_fill_manual(values=c("deepskyblue3","darkviolet"))  + labs(x="Proportion of gene body", y="Number of apaQTLs", title="Metagene plot for apaQTL SNP location")

Version Author Date
c5bf3fd brimittleman 2019-07-02

Density plot

propgenebodyplot=ggplot(genepropboth, aes(x=propGene,fill=Fraction)) + geom_histogram(bins=100,aes(y = (..count..)/sum(..count..))) + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")+ scale_fill_manual(values=c("deepskyblue3","darkviolet"))  + labs(y="Proportion of qtls",x="Proportion of gene body", title="Metagene plot for apaQTL SNP location")+  theme(text = element_text(size=16),legend.position = "bottom", axis.text.x =element_text(size=14), axis.text.y=element_text(size=14)) + facet_grid(~Fraction)
propgenebodyplot

geneprop_nuc=genepropboth %>% filter(Fraction=="Nuclear")

ggplot(geneprop_nuc, aes(x=propGene)) + geom_density(bins=100, fill="#7570B3") + geom_vline(xintercept =0,color= "black") + geom_vline(xintercept =1,color= "black")  + labs(x="Proportion of gene body", title="apaQTL SNP location")+  theme(text = element_text(size=16), axis.text.x =element_text(size=14), axis.text.y=element_text(size=14))
Warning: Ignoring unknown parameters: bins


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

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 [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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cowplot_0.9.4   forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1  
 [5] purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.1   
 [9] ggplot2_3.1.1   tidyverse_1.2.1 workflowr_1.4.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       cellranger_1.1.0 plyr_1.8.4       compiler_3.5.1  
 [5] pillar_1.3.1     git2r_0.25.2     highr_0.7        tools_3.5.1     
 [9] digest_0.6.18    lubridate_1.7.4  jsonlite_1.6     evaluate_0.12   
[13] nlme_3.1-137     gtable_0.2.0     lattice_0.20-38  pkgconfig_2.0.2 
[17] rlang_0.4.0      cli_1.1.0        rstudioapi_0.10  yaml_2.2.0      
[21] haven_1.1.2      withr_2.1.2      xml2_1.2.0       httr_1.3.1      
[25] knitr_1.20       hms_0.4.2        generics_0.0.2   fs_1.3.1        
[29] rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5 glue_1.3.0      
[33] R6_2.3.0         readxl_1.1.0     rmarkdown_1.10   reshape2_1.4.3  
[37] modelr_0.1.2     magrittr_1.5     whisker_0.3-2    backports_1.1.2 
[41] scales_1.0.0     htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0
[45] colorspace_1.3-2 labeling_0.3     stringi_1.2.4    lazyeval_0.2.1  
[49] munsell_0.5.0    broom_0.5.1      crayon_1.3.4