Overlap molQTLs, Opposite Direction

Last updated: 2018-10-08

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File	Version	Author	Date	Message
Rmd	11f9dfa	Briana Mittleman	2018-10-08	overlap molQTL opp dir

In the OverlapMolQTL analysis I looked at significant molecular QTLs and asked if they are also significant snp:gene pairs in the ApaQTLs. In this analysis, I will look at the significant ApaQTLs and ask if the snp:gene pairs are significant in the other molecular phenotypes. I expect enrichment of low pvalues in protQTLs but less in RNA.

I am going to complete this analysis first for the totalAPA QTLs.

library(workflowr)

This is workflowr version 1.1.1
Run ?workflowr for help getting started

library(reshape2)
library(tidyverse)

── Attaching packages ───────────────────────────────────────────────── tidyverse 1.2.1 ──

✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0

── Conflicts ──────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(VennDiagram)

Loading required package: grid

Loading required package: futile.logger

library(data.table)


Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

The following object is masked from 'package:purrr':

    transpose

The following objects are masked from 'package:reshape2':

    dcast, melt

library(qvalue)

MolQTL pvalues for Total ApaQTLs

sigTotAPAinMolPheno.R

#!/bin/rscripts

#this script creates takes in the permuted APAQTL results for the total fraction and nominal pvalues from the molecular phenotpye  molecular phenotype 

library(dplyr)
library(tidyr)
library(ggplot2)
library(readr)
library(optparse)

geneNames=read.table("/project2/gilad/briana/genome_anotation_data/ensemble_to_genename.txt", sep="\t", header=T, stringsAsFactors = F)

tot_perm=read.table("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_transcript_permResBH.txt", header = T,stringsAsFactors=F)

sigSNPgene=tot_perm %>% filter(-log10(bh)>1) %>% separate(pid, into=c("chr", "start", "end", "id"), sep=":") %>% separate(id, into=c("Gene.name", "strand", "peaknum"), sep="_") %>% dplyr::select(Gene.name, sid, bh) %>% group_by(Gene.name) %>% top_n(-1, bh) %>% ungroup() %>% dplyr::select(Gene.name, sid)

option_list = list(
    make_option(c("-M", "--molNom"), action="store", default=NA, type='character', help="molecular Nom results"),
    make_option(c("-O", "--output"), action="store", default=NA, type='character', help="output file for total APA sig snps in mol qtl")
)

opt_parser <- OptionParser(option_list=option_list)
opt <- parse_args(opt_parser)


if (opt$molNom == "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out") {
  in_file=read.table(opt$molNom, col.names = c("Gene.stable.ID", "sid", "dist", "pval", "slope"),stringsAsFactors=F)
  file_newNames=in_file %>%  inner_join(geneNames, by="Gene.stable.ID") %>% dplyr::select("Gene.name", "sid", "pval")
} else {
in_file=read.table(opt$molNom, col.names = c("pid", "sid", "dist", "pval", "slope"),stringsAsFactors=F)
file_newNames=in_file %>% separate(pid, into=c("Gene.stable.ID", "ver"), sep ="[.]") %>% inner_join(geneNames, by="Gene.stable.ID") %>% dplyr::select("Gene.name", "sid", "pval")
}

overlap= file_newNames %>% semi_join(sigSNPgene, by=c("Gene.name", "sid")) 

write.table(overlap, file=opt$output, quote=F, col.names = T, row.names = F)

Run this first on the rnaQTLs.

run_sigTotAPAinMolPhenoRNA.sh

#!/bin/bash


#SBATCH --job-name=run_sigTotAPAinMolPhenoRNA
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigTotAPAinMolPhenoRNA.out
#SBATCH --error=run_sigTotAPAinMolPhenoRNA.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPvalRNA.txt"

run_sigTotAPAinMolPhenoProt.sh

#!/bin/bash


#SBATCH --job-name=run_sigTotAPAinMolPhenoProt
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigTotAPAinMolPhenoProt.out
#SBATCH --error=run_sigTotAPAinMolPhenoProt.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPvalProtein.txt"

run_sigTotAPAinMolPhenoProt.sh

#!/bin/bash


#SBATCH --job-name=run_sigTotAPAinMolPhenoProt
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigTotAPAinMolPhenoProt.out
#SBATCH --error=run_sigTotAPAinMolPhenoProt.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPvalProtein.txt"

run_sigTotAPAinMolPhenoRNAg.sh

#!/bin/bash


#SBATCH --job-name=run_sigTotAPAinMolPhenoRNAg
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigTotAPAinMolPhenoRNAg.out
#SBATCH --error=run_sigTotAPAinMolPhenoRNAg.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseqGeuvadis.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPvalRNAg.txt"

run_sigTotAPAinMolPhenoRibo.sh

#!/bin/bash


#SBATCH --job-name=run_sigTotAPAinMolPhenoRibo
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigTotAPAinMolPhenoRibo.out
#SBATCH --error=run_sigTotAPAinMolPhenoRibo.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPvalribo.txt"

run_sigTotAPAinMolPheno4su.sh

#!/bin/bash


#SBATCH --job-name=run_sigTotAPAinMolPheno4su
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigTotAPAinMolPheno4su.out
#SBATCH --error=run_sigTotAPAinMolPheno4su.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su30.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPval4su30.txt" 

Rscript sigTotAPAinMolPheno.R --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su60.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molTotal/TotAPAqtlsPval4su60.txt"

MolQTL pvalues for Nuclear ApaQTLs

sigNucAPAinMolPheno.R

#!/bin/rscripts

#this script creates takes in the permuted APAQTL results for the total fraction and nominal pvalues from the molecular phenotpye  molecular phenotype 

library(dplyr)
library(tidyr)
library(ggplot2)
library(readr)
library(optparse)

geneNames=read.table("/project2/gilad/briana/genome_anotation_data/ensemble_to_genename.txt", sep="\t", header=T, stringsAsFactors = F)

nuc_perm=read.table("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_transcript_permResBH.txt", header = T,stringsAsFactors=F)

sigSNPgene=nuc_perm %>% filter(-log10(bh)>1) %>% separate(pid, into=c("chr", "start", "end", "id"), sep=":") %>% separate(id, into=c("Gene.name", "strand", "peaknum"), sep="_") %>% dplyr::select(Gene.name, sid, bh) %>% group_by(Gene.name) %>% top_n(-1, bh) %>% ungroup() %>% dplyr::select(Gene.name, sid)

option_list = list(
    make_option(c("-M", "--molNom"), action="store", default=NA, type='character', help="molecular Nom results"),
    make_option(c("-O", "--output"), action="store", default=NA, type='character', help="output file for total APA sig snps in mol qtl")
)

opt_parser <- OptionParser(option_list=option_list)
opt <- parse_args(opt_parser)


if (opt$molNom == "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out") {
  in_file=read.table(opt$molNom, col.names = c("Gene.stable.ID", "sid", "dist", "pval", "slope"),stringsAsFactors=F)
  file_newNames=in_file %>%  inner_join(geneNames, by="Gene.stable.ID") %>% dplyr::select("Gene.name", "sid", "pval")
} else {
in_file=read.table(opt$molNom, col.names = c("pid", "sid", "dist", "pval", "slope"),stringsAsFactors=F)
file_newNames=in_file %>% separate(pid, into=c("Gene.stable.ID", "ver"), sep ="[.]") %>% inner_join(geneNames, by="Gene.stable.ID") %>% dplyr::select("Gene.name", "sid", "pval")
}

overlap= file_newNames %>% semi_join(sigSNPgene, by=c("Gene.name", "sid")) 

write.table(overlap, file=opt$output, quote=F, col.names = T, row.names = F)

1 bash script for all of the phenotypes

run_sigNucAPAinMolPheno.sh

#!/bin/bash


#SBATCH --job-name=run_sigNucAPAinMolPheno
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_sigNucAPAinMolPheno.out
#SBATCH --error=run_sigNucAPAinMolPheno.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END

module load R 


Rscript run_sigNucAPAinMolPheno.sh --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molNuclear/NucAPAqtlsPvalRNA.txt" 


Rscript run_sigNucAPAinMolPheno.sh --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molNuclear/NucAPAqtlsPvalProtein.txt"  

Rscript run_sigNucAPAinMolPheno.sh --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseqGeuvadis.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molNuclear/NucAPAqtlsPvalRNAg.txt" 


Rscript run_sigNucAPAinMolPheno.sh --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molNuclear/NucAPAqtlsPvalribo.txt" 



Rscript run_sigNucAPAinMolPheno.sh --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su30.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molNuclear/NucAPAqtlsPval4su30.txt" 

Rscript run_sigNucAPAinMolPheno.sh --molNom "/project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su60.fixed.nominal.out" --output "/project2/gilad/briana/threeprimeseq/data/molecular_overlap/APA2molNuclear/NucAPAqtlsPval4su60.txt"

Create Histograms

I will next estimate sharing with pi_1 and create histograms of the resulting pvalues.
* Protein

totAPAinProt=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPvalProtein.txt", header = T, stringsAsFactors = F)
qval_prot=pi0est(totAPAinProt$pval, pi0.method = "bootstrap")
hist(totAPAinProt$pval)
text(.8,10, paste("pi_1=", round((1-qval_prot$pi0), digit=3), sep=" "))

* RNA

totAPAinRNA=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPvalRNA.txt", header = T, stringsAsFactors = F)
qval_RNA=pi0est(totAPAinRNA$pval, pi0.method = "bootstrap")
hist(totAPAinRNA$pval)
text(.8,18, paste("pi_1=", round((1-qval_RNA$pi0), digit=3), sep=" "))

Session information

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] qvalue_2.12.0       data.table_1.11.8   VennDiagram_1.6.20 
 [4] futile.logger_1.4.3 forcats_0.3.0       stringr_1.3.1      
 [7] dplyr_0.7.6         purrr_0.2.5         readr_1.1.1        
[10] tidyr_0.8.1         tibble_1.4.2        ggplot2_3.0.0      
[13] tidyverse_1.2.1     reshape2_1.4.3      workflowr_1.1.1    

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4     splines_3.5.1        haven_1.1.2         
 [4] lattice_0.20-35      colorspace_1.3-2     htmltools_0.3.6     
 [7] yaml_2.2.0           rlang_0.2.2          R.oo_1.22.0         
[10] pillar_1.3.0         glue_1.3.0           withr_2.1.2         
[13] R.utils_2.7.0        lambda.r_1.2.3       modelr_0.1.2        
[16] readxl_1.1.0         bindrcpp_0.2.2       bindr_0.1.1         
[19] plyr_1.8.4           munsell_0.5.0        gtable_0.2.0        
[22] cellranger_1.1.0     rvest_0.3.2          R.methodsS3_1.7.1   
[25] evaluate_0.11        knitr_1.20           broom_0.5.0         
[28] Rcpp_0.12.19         formatR_1.5          backports_1.1.2     
[31] scales_1.0.0         jsonlite_1.5         hms_0.4.2           
[34] digest_0.6.17        stringi_1.2.4        rprojroot_1.3-2     
[37] cli_1.0.1            tools_3.5.1          magrittr_1.5        
[40] lazyeval_0.2.1       futile.options_1.0.1 crayon_1.3.4        
[43] whisker_0.3-2        pkgconfig_2.0.2      xml2_1.2.0          
[46] lubridate_1.7.4      assertthat_0.2.0     rmarkdown_1.10      
[49] httr_1.3.1           rstudioapi_0.8       R6_2.3.0            
[52] nlme_3.1-137         git2r_0.23.0         compiler_3.5.1

This reproducible R Markdown analysis was created with workflowr 1.1.1

Overlap molQTLs, Opposite Direction

Briana Mittleman

10/8/2018

MolQTL pvalues for Total ApaQTLs

MolQTL pvalues for Nuclear ApaQTLs

Create Histograms

Session information