/
locusZoom.Rmd
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locusZoom.Rmd
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---
title: "LocusZoom Plot"
author: "Briana Mittleman"
date: "11/15/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
In this analysis I will create locus zoom plots for the example QTLs that look to be associated in APA and protein but not in RNA.
##EIF2A
I will first do this for the EIF2A totalAPA example. peak228606, 3:150302010.
To run this analysis, I will need the nominal pvalues for this peak/gene. I can then plot the snp location against the pvalue. After I have this working, I can add the r2 values.
EIF2A==ENSG00000144895
grep EIF2A /project2/gilad/briana/genome_anotation_data/ensemble_to_genename.txt
```{bash,eval=F}
grep peak228606 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak228606.EIF2A.nomTotal.txt
grep ENSG00000144895 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/RNA.EIF2A.nomTotal.txt
grep ENSG00000144895 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Prot.EIF2A.nomTotal.txt
grep ENSG00000144895 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Ribo.EIF2A.nomTotal.txt
```
FastQTL results for nominal:
* phenoID
* SID
* Distance
* Nominal Pval
* Slope
Librarys
```{r}
library(workflowr)
library(reshape2)
library(tidyverse)
library(VennDiagram)
library(data.table)
library(ggpubr)
library(cowplot)
```
```{r}
APA=read.table("../data/LocusZoom/TotalAPA.peak228606.EIF2A.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APAPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APAPval)
APA$Location=as.integer(APA$Location)
Prot=read.table("../data/LocusZoom/Prot.EIF2A.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "ProtPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, ProtPval)
Prot$Location=as.integer(Prot$Location)
RNA=read.table("../data/LocusZoom/RNA.EIF2A.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RnaPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RnaPval)
RNA$Location=as.integer(RNA$Location)
Ribo=read.table("../data/LocusZoom/Ribo.EIF2A.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RiboPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RiboPval)
Ribo$Location=as.integer(Ribo$Location)
```
I can join these by the snps that are tested for all three.
```{r}
allPheno=APA %>% inner_join(Prot, by="Location") %>% inner_join(Ribo, by="Location") %>% inner_join(RNA, by="Location")
```
First I can just plot these as is and see what happens:
```{r}
allPhen_melt= melt(allPheno, id.vars="Location")
```
```{r}
ggplot(allPhen_melt,aes(x=Location, y=value)) + geom_point() + facet_grid( rows=vars(variable))
```
I need to zoom in around my locus 150302010
```{r}
allPheno_filt=allPheno %>% filter(Location> 150297010 & Location < 150307010)
allPhen_filt_melt= melt(allPheno_filt, id.vars="Location")
ggplot(allPhen_filt_melt,aes(x=Location, y=-log10(value))) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=150302010, linetype="dashed", color = "red") + theme(axis.line=element_line()) + theme(panel.grid.major = element_line("lightgray",0.25), panel.grid.minor = element_line("lightgray",0.25)) + labs(x="Chromosome 3 Location", y="-Log 10 Pvalue", title="Locus Zoom for EIF2A:peak228606")
```
Plot each seperatly because power is different.
```{r}
ggplot(allPhen_filt_melt,aes(x=Location, y=-log10(value))) + geom_point() + facet_grid( rows=vars(variable),scales="free") + geom_vline(xintercept=150302010, linetype="dashed", color = "red") + theme(axis.line=element_line()) + theme(panel.grid.major = element_line("lightgray",0.25), panel.grid.minor = element_line("lightgray",0.25)) + labs(x="Chromosome 3 Location", y="-Log 10 Pvalue", title="Locus Zoom for EIF2A:peak228606")
```
The next step is to add the LD structure. I can do this with PLINK and the files I made for the GWAS overlap.
RunPlink_EIF2A.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RunPlink_EIF2A
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunPlink_EIF2A.out
#SBATCH --error=RunPlink_EIF2A.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load plink
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr3.ped --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr3.map --r2 --ld-snp 3:150302010 --ld-window-kb 1000 --ld-window 99999 --out /project2/gilad/briana/threeprimeseq/data/LocusZoom/EIF2A_leadsnp.txt
```
```{r}
LD_structure=read.table("../data/LocusZoom/EIF2A_leadsnp.txt.ld", header=T) %>% select(BP_B, R2)
colnames(LD_structure)=c("Location", "R2")
allPheno_filt2=allPheno %>% filter(Location> 150292010 & Location < 150312010)
allPheno_filt_LD=allPheno_filt2 %>% inner_join(LD_structure, by="Location")
allPheno_filt_LD_melt=melt(allPheno_filt_LD, id.vars=c("Location", "R2"))
```
```{r}
lockedscale=ggplot(allPheno_filt_LD_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=150302010, linetype="dashed", color = "red") + theme_linedraw()
freescale=ggplot(allPheno_filt_LD_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable), scales = "free") + geom_vline(xintercept=150302010, linetype="dashed", color = "red") + theme_linedraw()
```
```{r}
plot_grid(lockedscale,freescale, align = "v", ncol=1)
```
Try on the same plot:
```{r}
ggplot(allPheno_filt_LD_melt, aes(x=Location, y=-log10(value), col=variable, by =variable)) + geom_point() + geom_vline(xintercept=150302010, linetype="dashed", color = "red") + theme_linedraw()
```
rs14434 https://www.ncbi.nlm.nih.gov/variation/view/?q=rs14434&assm=GCF_000001405.33
##RINT1
RINT1 is a nuclear QTL. peak303436 7:105155320 ENSG00000135249
```{bash,eval=F}
grep peak303436 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak303436.RINT1.nomNuc.txt
grep peak303436 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak303436.RINT1.nomTotal.txt
grep ENSG00000135249 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/RNA.RINT1.nomTotal.txt
grep ENSG00000135249 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Prot.RINT1.nomTotal.txt
grep ENSG00000135249 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Ribo.RINT1.nomTotal.txt
```
RunPlink_RINT1.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RunPlink_RINT1
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunPlink_RINT1.out
#SBATCH --error=RunPlink_RINT1.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load plink
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr7.ped --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr7.map --r2 --ld-snp 7:105155320 --ld-window-kb 1000 --ld-window 99999 --out /project2/gilad/briana/threeprimeseq/data/LocusZoom/RINT1_leadsnp
```
```{r}
APA_Total_RINT1=read.table("../data/LocusZoom/TotalAPA.peak303436.RINT1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_TotalPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_TotalPval)
APA_Total_RINT1$Location=as.integer(APA_Total_RINT1$Location)
APA_Nuclear_RINT1=read.table("../data/LocusZoom/TotalAPA.peak303436.RINT1.nomNuc.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_NuclearPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_NuclearPval)
APA_Nuclear_RINT1$Location=as.integer(APA_Nuclear_RINT1$Location)
Prot_RINT1=read.table("../data/LocusZoom/Prot.RINT1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "ProtPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, ProtPval)
Prot_RINT1$Location=as.integer(Prot_RINT1$Location)
RNA_RINT1=read.table("../data/LocusZoom/RNA.RINT1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RnaPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RnaPval)
RNA_RINT1$Location=as.integer(RNA_RINT1$Location)
Ribo_RINT1=read.table("../data/LocusZoom/Ribo.RINT1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RiboPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RiboPval)
Ribo_RINT1$Location=as.integer(Ribo_RINT1$Location)
LD_structure_RINT1=read.table("../data/LocusZoom/RINT1_leadsnp.ld", header=T) %>% select(BP_B, R2)
colnames(LD_structure_RINT1)=c("Location", "R2")
```
I can join these by the snps that are tested for all three. Filter 1kb up and downstream
```{r}
allPheno_RINT1=APA_Total_RINT1 %>% inner_join(APA_Nuclear_RINT1, by="Location") %>% inner_join(Prot_RINT1, by="Location") %>% inner_join(Ribo_RINT1, by="Location") %>% inner_join(RNA_RINT1, by="Location") %>% inner_join(LD_structure_RINT1, by="Location") %>% filter(Location> 105154320 & Location < 105156320)
allPheno_RINT1_melt=melt(allPheno_RINT1, id.vars=c("Location", "R2"))
lockedscale_RINT1=ggplot(allPheno_RINT1_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=105155320, linetype="dashed", color = "red") + theme_linedraw()
freescale_RINT1=ggplot(allPheno_RINT1_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable), scales = "free") + geom_vline(xintercept=105155320, linetype="dashed", color = "red") + theme_linedraw()
plot_grid(lockedscale_RINT1,freescale_RINT1, align = "v", ncol=1)
```
rs2463632 (7:105155320): it is an intronic variant in PUS7
PUS7 chr7:105,080,108-105,162,714
RINT1 chr7:105,172,532-105,208,124
This snp is in the intron on the gene directly upstream of RINT1.
##LYAR
This is a nuclear QTL as well. peak235215 4:4196045 ENSG00000145220
RunLocusZoom_LYAR.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RunLocusZoom_LYAR
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunLocusZoom_LYAR.out
#SBATCH --error=RunLocusZoom_LYAR.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load plink
grep peak235215 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/NuclearAPA.peak303436.LYAR.nomNuc.txt
grep peak235215 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak303436.LYAR.nomTotal.txt
grep ENSG00000145220 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/RNA.LYAR.nomTotal.txt
grep ENSG00000145220 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Prot.LYAR.nomTotal.txt
grep ENSG00000145220 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Ribo.LYAR.nomTotal.txt
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr4.ped --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr4.map --r2 --ld-snp 4:4196045 --ld-window-kb 1000 --ld-window 99999 --out /project2/gilad/briana/threeprimeseq/data/LocusZoom/LYAR_leadsnp.txt
```
Move to my computer:
```{r}
APA_Total_LYAR=read.table("../data/LocusZoom/TotalAPA.peak303436.LYAR.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_TotalPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_TotalPval)
APA_Total_LYAR$Location=as.integer(APA_Total_LYAR$Location)
APA_Nuclear_LYAR=read.table("../data/LocusZoom/NuclearAPA.peak303436.LYAR.nomNuc.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_NuclearPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_NuclearPval)
APA_Nuclear_LYAR$Location=as.integer(APA_Nuclear_LYAR$Location)
Prot_LYAR=read.table("../data/LocusZoom/Prot.LYAR.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "ProtPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, ProtPval)
Prot_LYAR$Location=as.integer(Prot_LYAR$Location)
RNA_LYAR=read.table("../data/LocusZoom/RNA.LYAR.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RnaPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RnaPval)
RNA_LYAR$Location=as.integer(RNA_LYAR$Location)
Ribo_LYAR=read.table("../data/LocusZoom/Ribo.LYAR.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RiboPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RiboPval)
Ribo_LYAR$Location=as.integer(Ribo_LYAR$Location)
LD_structure_LYAR=read.table("../data/LocusZoom/LYAR_leadsnp.txt.ld", header=T) %>% select(BP_B, R2)
colnames(LD_structure_LYAR)=c("Location", "R2")
allPheno_LYAR=APA_Total_LYAR %>% inner_join(APA_Nuclear_LYAR, by="Location") %>% inner_join(Prot_LYAR, by="Location") %>% inner_join(Ribo_LYAR, by="Location") %>% inner_join(RNA_LYAR, by="Location") %>% inner_join(LD_structure_LYAR, by="Location") %>% filter(Location> 4191045 & Location < 4201045)
allPheno_LYAR_melt=melt(allPheno_LYAR, id.vars=c("Location", "R2"))
lockedscale_LYAR=ggplot(allPheno_LYAR_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=4196045, linetype="dashed", color = "red") + theme_linedraw()
freescale_LYAR=ggplot(allPheno_LYAR_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable), scales = "free") + geom_vline(xintercept=4196045, linetype="dashed", color = "red") + theme_linedraw()
plot_grid(lockedscale_LYAR,freescale_LYAR, align = "v", ncol=1)
```
Snp is in an intron OTOP1 gene 2 genes upstream. rs7682186
##PSMF1
Total QTL peak193648 20:1131308 ENSG00000125818
RunLocusZoom_PSMF1.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RunLocusZoom_PSMF1
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunLocusZoom_PSMF1.out
#SBATCH --error=RunLocusZoom_PSMF1.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load plink
grep peak193648 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/NuclearAPA.peak193648.PSMF1.nomNuc.txt
grep peak193648 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak193648.PSMF1.nomTotal.txt
grep ENSG00000125818 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/RNA.PSMF1.nomTotal.txt
grep ENSG00000125818 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Prot.PSMF1.nomTotal.txt
grep ENSG00000125818 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Ribo.PSMF1.nomTotal.txt
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr20.ped --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr20.map --r2 --ld-snp 20:1131308 --ld-window-kb 1000 --ld-window 99999 --out /project2/gilad/briana/threeprimeseq/data/LocusZoom/PSMF1_leadsnp.txt
```
Move to computer
```{r}
APA_Total_PSMF1=read.table("../data/LocusZoom/TotalAPA.peak193648.PSMF1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_TotalPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_TotalPval)
APA_Total_PSMF1$Location=as.integer(APA_Total_PSMF1$Location)
APA_Nuclear_PSMF1=read.table("../data/LocusZoom/NuclearAPA.peak193648.PSMF1.nomNuc.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_NuclearPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_NuclearPval)
APA_Nuclear_PSMF1$Location=as.integer(APA_Nuclear_PSMF1$Location)
Prot_PSMF1=read.table("../data/LocusZoom/Prot.PSMF1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "ProtPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, ProtPval)
Prot_PSMF1$Location=as.integer(Prot_PSMF1$Location)
RNA_PSMF1=read.table("../data/LocusZoom/RNA.PSMF1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RnaPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RnaPval)
RNA_PSMF1$Location=as.integer(RNA_PSMF1$Location)
Ribo_PSMF1=read.table("../data/LocusZoom/Ribo.PSMF1.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RiboPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RiboPval)
Ribo_PSMF1$Location=as.integer(Ribo_PSMF1$Location)
LD_structure_PSMF1=read.table("../data/LocusZoom/PSMF1_leadsnp.txt.ld", header=T) %>% select(BP_B, R2)
colnames(LD_structure_PSMF1)=c("Location", "R2")
allPheno_PSMF1=APA_Total_PSMF1 %>% inner_join(APA_Nuclear_PSMF1, by="Location") %>% inner_join(Prot_PSMF1, by="Location") %>% inner_join(Ribo_PSMF1, by="Location") %>% inner_join(RNA_PSMF1, by="Location") %>% inner_join(LD_structure_PSMF1, by="Location") %>% filter(Location> 1121308 & Location < 1181308)
allPheno_PSMF1_melt=melt(allPheno_PSMF1, id.vars=c("Location", "R2"))
lockedscale_PSMF1=ggplot(allPheno_PSMF1_melt, aes(x=Location, y=-log10(value),col=R2)) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=1131308, linetype="dashed", color = "red") + theme_linedraw()
freescale_PSMF1=ggplot(allPheno_PSMF1_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable), scales = "free") + geom_vline(xintercept=1131308, linetype="dashed", color = "red") + theme_linedraw()
plot_grid(lockedscale_PSMF1,freescale_PSMF1, align = "v", ncol=1)
```
This varriant is in an intron of the PSMF1 gene. rs56398212
##EBI3
This is a total and a nuclear QTL peak152751, ENSG00000105246 19:4236475
RunLocusZoom_EBI3.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RunLocusZoom_EBI3
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunLocusZoom_EBI3.out
#SBATCH --error=RunLocusZoom_EBI3.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load plink
grep peak152751 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/NuclearAPA.peak152751.EBI3.nomNuc.txt
grep peak152751 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak152751.EBI3.nomTotal.txt
grep ENSG00000105246 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/RNA.EBI3.nomTotal.txt
grep ENSG00000105246 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Prot.EBI3.nomTotal.txt
grep ENSG00000105246 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Ribo.EBI3.nomTotal.txt
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr19.ped --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr19.map --r2 --ld-snp 19:4236475 --ld-window-kb 1000 --ld-window 99999 --out /project2/gilad/briana/threeprimeseq/data/LocusZoom/EBI3_leadsnp.txt
```
Move to comp
```{r}
APA_Total_EBI3=read.table("../data/LocusZoom/TotalAPA.peak152751.EBI3.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_TotalPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_TotalPval)
APA_Total_EBI3$Location=as.integer(APA_Total_EBI3$Location)
APA_Nuclear_EBI3=read.table("../data/LocusZoom/NuclearAPA.peak152751.EBI3.nomNuc.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_NuclearPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_NuclearPval)
APA_Nuclear_EBI3$Location=as.integer(APA_Nuclear_EBI3$Location)
Prot_EBI3=read.table("../data/LocusZoom/Prot.EBI3.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "ProtPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, ProtPval)
Prot_EBI3$Location=as.integer(Prot_EBI3$Location)
RNA_EBI3=read.table("../data/LocusZoom/RNA.EBI3.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RnaPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RnaPval)
RNA_EBI3$Location=as.integer(RNA_EBI3$Location)
Ribo_EBI3=read.table("../data/LocusZoom/Ribo.EBI3.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RiboPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RiboPval)
Ribo_EBI3$Location=as.integer(Ribo_EBI3$Location)
LD_structure_EBI3=read.table("../data/LocusZoom/EBI3_leadsnp.txt.ld", header=T) %>% select(BP_B, R2)
colnames(LD_structure_EBI3)=c("Location", "R2")
allPheno_EBI3=APA_Total_EBI3 %>% inner_join(APA_Nuclear_EBI3, by="Location") %>% inner_join(Prot_EBI3, by="Location") %>% inner_join(Ribo_EBI3, by="Location") %>% inner_join(RNA_EBI3, by="Location") %>% inner_join(LD_structure_EBI3, by="Location") %>% filter(Location> 4231475 & Location < 4241475)
allPheno_EBI3_melt=melt(allPheno_EBI3, id.vars=c("Location", "R2"))
lockedscale_EBI3=ggplot(allPheno_EBI3_melt, aes(x=Location, y=-log10(value),col=R2)) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=4236475, linetype="dashed", color = "red") + theme_linedraw()
freescale_EBI3=ggplot(allPheno_EBI3_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable), scales = "free") + geom_vline(xintercept=4236475, linetype="dashed", color = "red") + theme_linedraw()
plot_grid(lockedscale_EBI3,freescale_EBI3, align = "v", ncol=1)
```
Snp is in the last intron of EBI3. It looks like the lead protien snp is the one directly upstream. rs353704. The region is CCCCAC. The preceeding SNP is rs353705. The relevent peak is 19:4236433:4236517. The snp is in the peak. This is interesting because the alternative allele decreases usage of this peak and the protein.
##SACM1L
There are 3 QTLs in the total and nuclear for this. I am gonig to focus on the hit that has the same snp peak assocaition.
peak216086 3:45780980 ENSG00000211456
RunLocusZoom_SACM1L.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RunLocusZoom_SACM1L
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunLocusZoom_SACM1L.out
#SBATCH --error=RunLocusZoom_SACM1L.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load plink
grep peak216086 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/NuclearAPA.peak216086.SACM1L.nomNuc.txt
grep peak216086 /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_NomRes.txt > /project2/gilad/briana/threeprimeseq/data/LocusZoom/TotalAPA.peak216086.SACM1L.nomTotal.txt
grep ENSG00000211456 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/RNA.SACM1L.nomTotal.txt
grep ENSG00000211456 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Prot.SACM1L.nomTotal.txt
grep ENSG00000211456 /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out > /project2/gilad/briana/threeprimeseq/data/LocusZoom/Ribo.SACM1L.nomTotal.txt
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr3.ped --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr3.map --r2 --ld-snp 3:45780980 --ld-window-kb 1000 --ld-window 99999 --out /project2/gilad/briana/threeprimeseq/data/LocusZoom/SACM1L_leadsnp.txt
```
.
Move to comp
```{r}
APA_Total_SACM1L=read.table("../data/LocusZoom/TotalAPA.peak216086.SACM1L.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_TotalPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_TotalPval)
APA_Total_SACM1L$Location=as.integer(APA_Total_SACM1L$Location)
APA_Nuclear_SACM1L=read.table("../data/LocusZoom/NuclearAPA.peak216086.SACM1L.nomNuc.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "APA_NuclearPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":") %>% select( Location, APA_NuclearPval)
APA_Nuclear_SACM1L$Location=as.integer(APA_Nuclear_SACM1L$Location)
Prot_SACM1L=read.table("../data/LocusZoom/Prot.SACM1L.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "ProtPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, ProtPval)
Prot_SACM1L$Location=as.integer(Prot_SACM1L$Location)
RNA_SACM1L=read.table("../data/LocusZoom/RNA.SACM1L.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RnaPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RnaPval)
RNA_SACM1L$Location=as.integer(RNA_SACM1L$Location)
Ribo_SACM1L=read.table("../data/LocusZoom/Ribo.SACM1L.nomTotal.txt", stringsAsFactors = F, col.names = c("PeakID", "SID", "Dist", "RiboPval","slope")) %>% separate(SID, into=c("Chrom", "Location"), sep=":")%>% select( Location, RiboPval)
Ribo_SACM1L$Location=as.integer(Ribo_SACM1L$Location)
LD_structure_SACM1L=read.table("../data/LocusZoom/SACM1L_leadsnp.txt.ld", header=T) %>% select(BP_B, R2)
colnames(LD_structure_SACM1L)=c("Location", "R2")
allPheno_SACM1L=APA_Total_SACM1L %>% inner_join(APA_Nuclear_SACM1L, by="Location") %>% inner_join(Prot_SACM1L, by="Location") %>% inner_join(Ribo_SACM1L, by="Location") %>% inner_join(RNA_SACM1L, by="Location") %>% inner_join(LD_structure_SACM1L, by="Location") %>% filter(Location> 45770980 & Location < 45790980)
allPheno_SACM1L_melt=melt(allPheno_SACM1L, id.vars=c("Location", "R2"))
lockedscale_SACM1L=ggplot(allPheno_SACM1L_melt, aes(x=Location, y=-log10(value),col=R2)) + geom_point() + facet_grid( rows=vars(variable)) + geom_vline(xintercept=45780980, linetype="dashed", color = "red") + theme_linedraw()
freescale_SACM1L=ggplot(allPheno_SACM1L_melt, aes(x=Location, y=-log10(value), col=R2)) + geom_point() + facet_grid( rows=vars(variable), scales = "free") + geom_vline(xintercept=45780980, linetype="dashed", color = "red") + theme_linedraw()
plot_grid(lockedscale_SACM1L,freescale_SACM1L, align = "v", ncol=1)
```
The snp is in an intron of the SAMCL1 gene rs80065472. The peak is in the UTR of the gene.