Overlap molQTLs, Opposite Direction

Last updated: 2018-10-09

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Rmd	605aa2d	Briana Mittleman	2018-10-09	plot results
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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)
set.seed(327)

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=broadwl
#SBATCH --mem=32G
#SBATCH --mail-type=END

module load R 


Rscript sigNucAPAinMolPheno.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/APA2molNuclear/NucAPAqtlsPvalRNA.txt" 


Rscript sigNucAPAinMolPheno.R  --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 sigNucAPAinMolPheno.R  --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 sigNucAPAinMolPheno.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/APA2molNuclear/NucAPAqtlsPvalribo.txt" 



Rscript sigNucAPAinMolPheno.R  --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 sigNucAPAinMolPheno.R  --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

Total

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")

totAPAinRNA=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPvalRNA.txt", header = T, stringsAsFactors = F)
qval_RNA=pi0est(totAPAinRNA$pval, pi0.method = "bootstrap")

RNA Geuvadis

totAPAinRNAg=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPvalRNAg.txt", header = T, stringsAsFactors = F)
qval_RNAg=pi0est(totAPAinRNAg$pval, pi0.method = "bootstrap")

*Ribo

totAPAinRibo=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPvalribo.txt", header = T, stringsAsFactors = F)
qval_Ribo=pi0est(totAPAinRibo$pval, pi0.method = "bootstrap")

4su30

totAPAinsu30=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPval4su30.txt", header = T, stringsAsFactors = F)
qval_su30=pi0est(totAPAinsu30$pval, pi0.method = "bootstrap")

4su60

totAPAinsu60=read.table("../data/mol_overlap/APA2molTotal/TotAPAqtlsPval4su60.txt", header = T, stringsAsFactors = F)
qval_su60=pi0est(totAPAinsu60$pval, pi0.method = "bootstrap")

All plots:

par(mfrow=c(2,3))
hist(totAPAinsu30$pval, xlab="4su30 Pvalue", main="Significant Total APA QTLs \n 4su30")
text(.6,15, paste("pi_1=", round((1-qval_su30$pi0), digit=3), sep=" "))
hist(totAPAinsu60$pval, xlab="4su60 Pvalue", main="Significant Total APA QTLs \n 4su60")
text(.6,15, paste("pi_1=", round((1-qval_su60$pi0), digit=3), sep=" "))
hist(totAPAinRNA$pval,  xlab="RNAPvalue", main="Significant Total APA QTLs \n RNA")
text(.6,18, paste("pi_1=", round((1-qval_RNA$pi0), digit=3), sep=" "))
hist(totAPAinRNAg$pval, xlab="RNA Guevadis Pvalue", main="Significant Total APA QTLs \n RNA Geuvadis")
text(.6,18, paste("pi_1=", round((1-qval_RNAg$pi0), digit=3), sep=" "))
hist(totAPAinRibo$pval, xlab="Ribo (Translation) Pvalue", main="Significant Total APA QTLs \n Ribo")
text(.6,15, paste("pi_1=", round((1-qval_Ribo$pi0), digit=3), sep=" "))
hist(totAPAinProt$pval,  xlab="Protein Pvalue", main="Significant Total APA QTLs \n Protein")
text(.6,10, paste("pi_1=", round((1-qval_prot$pi0), digit=3), sep=" "))

Nuclear