Last updated: 2019-06-20

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Knit directory: apaQTL/analysis/

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Unstaged changes:
    Modified:   analysis/Readdistagainstfeatures.Rmd
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    Deleted:    code/test.txt

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd eb847c1 brimittleman 2019-06-20 add analysis by pval
html ca379ce brimittleman 2019-06-13 Build site.
Rmd 2fd2b27 brimittleman 2019-06-13 fix bug
html b907ac1 brimittleman 2019-06-12 Build site.
Rmd 178c5dc brimittleman 2019-06-12 new geno
html 6b164c8 brimittleman 2019-06-07 Build site.
Rmd b39620d brimittleman 2019-06-07 add bonfor results
html 458e494 brimittleman 2019-06-07 Build site.
Rmd 32091ee brimittleman 2019-06-07 more prop explained to new analysis

library(tidyverse)
── Attaching packages ────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
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── Conflicts ───────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
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library(workflowr)
This is workflowr version 1.3.0
Run ?workflowr for help getting started
library(reshape2)

Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':

    smiths

I need to fix the explained_FDR10.sort.txt and unexplained_FDR10.sort.txt files because right now this file has multiple genes per snp.

python fixExandUnexeQTL.py ../data/Li_eQTLs/explained_FDR10.sort.txt ../data/Li_eQTLs/explained_FDR10.sort_FIXED.txt
python fixExandUnexeQTL.py ../data/Li_eQTLs/unexplained_FDR10.sort.txt ../data/Li_eQTLs/unexplained_FDR10.sort_FIXED.txt

There are 1195 explained and 814 unexplained eQTLs. I will next look at each of these in my apadata.

Convert nominal results to have snps rather than rsids:

python convertNominal2SNPLOC.py Total
python convertNominal2SNPLOC.py Nuclear
mkdir ../data/overlapeQTL_try2
sbatch run_getapafromeQTL.sh

total

I can group the unexplained by gene and snp then I can ask if there is at least 1 significat peak for each of these.

I will use the bonforoni correction here and multiply the pvalue by the number of peaks in the gene:snp association.

nomnames=c("peakID", 'snp','dist', 'pval', 'slope')
totalapaUnexplained=read.table("../data/overlapeQTL_try2/apaTotal_unexplainedQTLs.txt", stringsAsFactors = F, col.names = nomnames)
totalapaUnexplained=totalapaUnexplained %>% separate(peakID, into=c("chr","start","end","geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc", "strand", "PASnum"), sep="_") %>% group_by(gene, snp)  %>% mutate(nPeaks=n(), adjPval=pval* nPeaks)%>%  dplyr::slice(which.min(adjPval))

totalapaUnexplained_sig= totalapaUnexplained %>% filter(adjPval<.05)

Look at distribution of these pvals:

ggplot(totalapaUnexplained, aes(x=adjPval)) + geom_histogram(bins=50)

Version Author Date
ca379ce brimittleman 2019-06-13
b907ac1 brimittleman 2019-06-12

Proportion explained:

nrow(totalapaUnexplained_sig)/nrow(totalapaUnexplained)
[1] 0.1632653

I tested 588 unexplained eQTLs in the total fraction and 96 have a bonforoni corrected significant peak.

Compare to explained eQTLS:

totalapaexplained=read.table("../data/overlapeQTL_try2/apaTotal_explainedQTLs.txt", stringsAsFactors = F, col.names = nomnames) %>% separate(peakID, into=c("chr","start","end","geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc", "strand", "PASnum"), sep="_") %>% group_by(gene, snp) %>%  mutate(nPeaks=n(), adjPval=pval* nPeaks) %>%  dplyr::slice(which.min(adjPval))

totalapaexplained_sig= totalapaexplained %>% filter(adjPval<.05)

nrow(totalapaexplained_sig)/nrow(totalapaexplained)
[1] 0.1304878

I am testing 820 explained eQTLs and of those 107 have a bonforoni corrected significant peak.

difference of proportions:

prop.test(x=c(nrow(totalapaUnexplained_sig),nrow(totalapaexplained_sig)), n=c(nrow(totalapaUnexplained),nrow(totalapaexplained)))

    2-sample test for equality of proportions with continuity
    correction

data:  c(nrow(totalapaUnexplained_sig), nrow(totalapaexplained_sig)) out of c(nrow(totalapaUnexplained), nrow(totalapaexplained))
X-squared = 2.722, df = 1, p-value = 0.09898
alternative hypothesis: two.sided
95 percent confidence interval:
 -0.00641871  0.07197371
sample estimates:
   prop 1    prop 2 
0.1632653 0.1304878 
ggplot(totalapaUnexplained_sig,aes(x=loc)) + geom_histogram(stat="count",aes(y=..count../sum(..count..))) + labs(y="Proportion", title = "Total apaQTLs explaining eQTLs")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Version Author Date
ca379ce brimittleman 2019-06-13
b907ac1 brimittleman 2019-06-12
totalapaUnexplained_sig_loc= totalapaUnexplained_sig %>% group_by(loc) %>% summarise(nLocTotalUn=n()) %>% mutate(propTotalUn=nLocTotalUn/nrow(totalapaUnexplained_sig))
totalapaexplained_sig_loc= totalapaexplained_sig %>% group_by(loc) %>% summarise(nLocTotalEx=n()) %>% mutate(propTotalEx=nLocTotalEx/nrow(totalapaexplained_sig))

BothTotalLoc=totalapaUnexplained_sig_loc %>% full_join(totalapaexplained_sig_loc,by="loc") %>%  replace_na(list(propTotalUn = 0, nLocTotalUn = 0,propTotalEx=0,nLocTotalEx=0  ))

BothTotalLoc
# A tibble: 5 x 5
  loc    nLocTotalUn propTotalUn nLocTotalEx propTotalEx
  <chr>        <dbl>       <dbl>       <dbl>       <dbl>
1 cds              7      0.0729           8      0.0748
2 end              9      0.0938           7      0.0654
3 intron          17      0.177           20      0.187 
4 utr3            59      0.615           70      0.654 
5 utr5             4      0.0417           2      0.0187

nuclear

nuclearapaUnexplained=read.table("../data/overlapeQTL_try2/apaNuclear_unexplainedQTLs.txt", stringsAsFactors = F, col.names = nomnames) %>% separate(peakID, into=c("chr","start","end","geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc", "strand", "PASnum"), sep="_") %>% group_by(gene, snp)  %>%  mutate(nPeaks=n(), adjPval=pval* nPeaks) %>% dplyr::slice(which.min(adjPval))

nuclearapaUnexplained_sig= nuclearapaUnexplained %>% filter(adjPval<.05)

nrow(nuclearapaUnexplained_sig)/nrow(nuclearapaUnexplained)
[1] 0.1649832

I tested 594 unexplained eQTLs in the nuclear fraction and 98 have a bonforoni corrected significant peak.

nuclearapaexplained=read.table("../data/overlapeQTL_try2/apaNuclear_explainedQTLs.txt", stringsAsFactors = F, col.names = nomnames) %>% separate(peakID, into=c("chr","start","end","geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc", "strand", "PASnum"), sep="_") %>% group_by(gene, snp) %>%  mutate(nPeaks=n(), adjPval=pval* nPeaks) %>%  dplyr::slice(which.min(adjPval))

nuclearapaexplained_sig= nuclearapaexplained %>% filter(adjPval<.05)

nrow(nuclearapaexplained_sig)/nrow(nuclearapaexplained)
[1] 0.13269

I tested 829 explained eQTLs in the nuclear fraction and 110 have a nominally significant peak. difference of proportions:

prop.test(x=c(nrow(nuclearapaUnexplained_sig),nrow(nuclearapaexplained_sig)), n=c(nrow(nuclearapaUnexplained),nrow(nuclearapaexplained)))

    2-sample test for equality of proportions with continuity
    correction

data:  c(nrow(nuclearapaUnexplained_sig), nrow(nuclearapaexplained_sig)) out of c(nrow(nuclearapaUnexplained), nrow(nuclearapaexplained))
X-squared = 2.6386, df = 1, p-value = 0.1043
alternative hypothesis: two.sided
95 percent confidence interval:
 -0.006890426  0.071476780
sample estimates:
   prop 1    prop 2 
0.1649832 0.1326900 
ggplot(nuclearapaUnexplained_sig,aes(x=loc))  + geom_histogram(stat="count",aes(y=..count../sum(..count..))) + labs(title = "Nuclear apaQTLs explaining eQTLs", y="Proportion")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Version Author Date
ca379ce brimittleman 2019-06-13
b907ac1 brimittleman 2019-06-12
nuclearapaUnexplained_sig_loc= nuclearapaUnexplained_sig %>% group_by(loc) %>% summarise(nLocnuclearUn=n()) %>% mutate(propnuclearUn=nLocnuclearUn/nrow(nuclearapaUnexplained_sig))
nuclearapaexplained_sig_loc= nuclearapaexplained_sig %>% group_by(loc) %>% summarise(nLocnuclearEx=n()) %>% mutate(propnuclearEx=nLocnuclearEx/nrow(nuclearapaexplained_sig))

BothnuclearLoc=nuclearapaUnexplained_sig_loc %>% full_join(nuclearapaexplained_sig_loc,by="loc") %>%  replace_na(list(propnuclearUn = 0, nLocnuclearUn = 0,propnuclearEx=0,nLocnuclearEx=0  ))

BothnuclearLoc
# A tibble: 5 x 5
  loc    nLocnuclearUn propnuclearUn nLocnuclearEx propnuclearEx
  <chr>          <dbl>         <dbl>         <dbl>         <dbl>
1 cds                4        0.0408             3        0.0273
2 end               10        0.102              9        0.0818
3 intron            18        0.184             33        0.3   
4 utr3              66        0.673             63        0.573 
5 utr5               0        0                  2        0.0182
prop.test(x=c(18,33), n=c(nrow(nuclearapaUnexplained_sig),nrow(nuclearapaexplained_sig)))

    2-sample test for equality of proportions with continuity
    correction

data:  c(18, 33) out of c(nrow(nuclearapaUnexplained_sig), nrow(nuclearapaexplained_sig))
X-squared = 3.1869, df = 1, p-value = 0.07423
alternative hypothesis: two.sided
95 percent confidence interval:
 -0.240913267  0.008260206
sample estimates:
   prop 1    prop 2 
0.1836735 0.3000000 
prop.test(x=c(66,63), n=c(nrow(nuclearapaUnexplained_sig),nrow(nuclearapaexplained_sig)))

    2-sample test for equality of proportions with continuity
    correction

data:  c(66, 63) out of c(nrow(nuclearapaUnexplained_sig), nrow(nuclearapaexplained_sig))
X-squared = 1.8258, df = 1, p-value = 0.1766
alternative hypothesis: two.sided
95 percent confidence interval:
 -0.03992433  0.24140856
sample estimates:
   prop 1    prop 2 
0.6734694 0.5727273 

total v nuclear

prop.test(x=c(nrow(nuclearapaUnexplained_sig),nrow(totalapaUnexplained_sig)), n=c(nrow(nuclearapaUnexplained),nrow(totalapaUnexplained)))

    2-sample test for equality of proportions with continuity
    correction

data:  c(nrow(nuclearapaUnexplained_sig), nrow(totalapaUnexplained_sig)) out of c(nrow(nuclearapaUnexplained), nrow(totalapaUnexplained))
X-squared = 1.4301e-06, df = 1, p-value = 0.999
alternative hypothesis: two.sided
95 percent confidence interval:
 -0.04220475  0.04564046
sample estimates:
   prop 1    prop 2 
0.1649832 0.1632653 

Differences in proportion by location

allLocProp=BothnuclearLoc %>% full_join(BothTotalLoc, by="loc") %>% select(loc,propnuclearUn,propnuclearEx,propTotalUn,propTotalEx )

allLocPropmelt= melt(allLocProp, id.vars = "loc") %>% mutate(Fraction=ifelse(grepl("Total", variable), "Total", "Nuclear"),eQTL=ifelse(grepl("Un", variable), "Unexplained", "Explained"))


ggplot(allLocPropmelt,aes(x=loc, fill=eQTL, y=value)) + geom_histogram(stat="identity", position = "dodge") + facet_grid(~Fraction)+ labs(y="Proportion of PAS", title="apaQTLs overlaping eQTLs by PAS location")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Version Author Date
ca379ce brimittleman 2019-06-13
b907ac1 brimittleman 2019-06-12

This is a very stringent test. A less stringent way to get an upper bound would be to make an informed decision about which peak to use. This will make it so I am only testing one PAS per gene.

Vary the pvalue cuttoff

To test if .05 is a good cuttoff for this analysis I will create a function that computes the overlap at different cutoffs. I will go from .01 to .5 by .05

totalapaUnexplained totalapaexplained

nuclearapaUnexplained nuclearapaexplained

prop_overlap=function(status, fraction, cutoff){
  if (fraction=="Total"){
    if (status=="Explained"){
      file=totalapaexplained
      sig=file %>% filter(adjPval<=cutoff)
      proportion=nrow(sig)/nrow(file)
    }else {
      file=totalapaUnexplained
      sig=file %>% filter(adjPval<=cutoff)
      proportion=nrow(sig)/nrow(file)
    }
  } else{
    if (status=="Explained"){
      file=nuclearapaexplained
      sig=file %>% filter(adjPval<=cutoff)
      proportion=nrow(sig)/nrow(file)
     }else {
      file=nuclearapaUnexplained
      sig=file %>% filter(adjPval<=cutoff)
      proportion=nrow(sig)/nrow(file)
     }
  }
  return(proportion)
}
cutoffs=c(0.001,0.01,0.02,0.03,0.04,0.05,0.1,0.2,0.3,0.4,0.5)

TotalExplained_Proportions=c()
for(i in cutoffs){
  TotalExplained_Proportions=c( TotalExplained_Proportions, prop_overlap("Explained", "Total", i))
}
TotalExplained_ProportionsDF=as.data.frame(cbind(cutoffs,Prop=TotalExplained_Proportions, Status=rep("Explained", 11), Fraction=rep("Total", 11)))

TotalUnexplained_Proportions=c()
for(i in cutoffs){
  TotalUnexplained_Proportions=c(TotalUnexplained_Proportions, prop_overlap("Unexplained", "Total", i))
}
TotalUnexplained_ProportionsDF=as.data.frame(cbind(cutoffs,Prop=TotalUnexplained_Proportions, Status=rep("Unexplained", 11), Fraction=rep("Total", 11)))

NuclearExplained_Proportions=c()
for(i in cutoffs){
  NuclearExplained_Proportions=c( NuclearExplained_Proportions, prop_overlap("Explained", "Nuclear", i))
}
NuclearExplained_ProportionsDF=as.data.frame(cbind(cutoffs,Prop=NuclearExplained_Proportions, Status=rep("Explained", 11), Fraction=rep("Nuclear", 11)))


NuclearUnexplained_Proportions=c()
for(i in cutoffs){
  NuclearUnexplained_Proportions=c( NuclearUnexplained_Proportions, prop_overlap("Unexplained", "Nuclear", i))
}
NuclearUnexplained_ProportionsDF=as.data.frame(cbind(cutoffs,Prop=NuclearUnexplained_Proportions, Status=rep("Unexplained", 11), Fraction=rep("Nuclear", 11)))



AllPropDF=bind_rows(TotalExplained_ProportionsDF,TotalUnexplained_ProportionsDF,NuclearExplained_ProportionsDF,NuclearUnexplained_ProportionsDF)
Warning in bind_rows_(x, .id): Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
Warning in bind_rows_(x, .id): Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
Warning in bind_rows_(x, .id): Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
AllPropDF$Prop=as.numeric(AllPropDF$Prop)

Plot this:

ggplot(AllPropDF, aes(x=cutoffs, y=Prop, fill=Status)) + geom_bar(position = "dodge", stat="identity") + facet_grid(~Fraction)


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

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=en_US.UTF-8   
 [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] reshape2_1.4.3  workflowr_1.3.0 forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1     tidyr_0.8.3    
 [9] tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       cellranger_1.1.0 pillar_1.3.1     compiler_3.5.1  
 [5] git2r_0.25.2     plyr_1.8.4       tools_3.5.1      digest_0.6.18   
 [9] lubridate_1.7.4  jsonlite_1.6     evaluate_0.12    nlme_3.1-137    
[13] gtable_0.2.0     lattice_0.20-38  pkgconfig_2.0.2  rlang_0.3.1     
[17] cli_1.0.1        rstudioapi_0.10  yaml_2.2.0       haven_1.1.2     
[21] withr_2.1.2      xml2_1.2.0       httr_1.3.1       knitr_1.20      
[25] hms_0.4.2        generics_0.0.2   fs_1.2.6         rprojroot_1.3-2 
[29] grid_3.5.1       tidyselect_0.2.5 glue_1.3.0       R6_2.3.0        
[33] fansi_0.4.0      readxl_1.1.0     rmarkdown_1.10   modelr_0.1.2    
[37] magrittr_1.5     whisker_0.3-2    backports_1.1.2  scales_1.0.0    
[41] htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0 colorspace_1.3-2
[45] labeling_0.3     utf8_1.1.4       stringi_1.2.4    lazyeval_0.2.1  
[49] munsell_0.5.0    broom_0.5.1      crayon_1.3.4