Last updated: 2018-09-25

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Untracked files:
    Untracked:  analysis/callMolQTLS.Rmd
    Untracked:  analysis/ncbiRefSeq_sm.sort.mRNA.bed
    Untracked:  analysis/snake.config.notes.Rmd
    Untracked:  analysis/verifyBAM.Rmd
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    Untracked:  data/APApeaksYL.total.inbrain.bed
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Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/overlap_qtls.Rmd
    Modified:   analysis/peakOverlap_oppstrand.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   code/Snakefile
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Expand here to see past versions:
    File Version Author Date Message
    Rmd f4e1942 Briana Mittleman 2018-09-25 initiate all ind QTL analysis

I am using the code from peakOverlap_oppstrand.Rmd analysis to call QTLs on the full set of individuals. (still missing 4 due to genotype issues- Remove 18500, 19092 and 19193, 18497 - at 35).

Scripts:
* APAqtl_nominal_oppstrand.sh

  • APAqtl_perm_Opp.sh

Write a script to ad the BH correction of the permuted QTL pvalues. I will write the plots to

APAqtlpermCorrectQQplot.R

library(tidyverse)
library(workflowr)
library(cowplot)
library(reshape2)

##total results
tot.perm= read.table("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_Opp/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_permRes.txt",head=F, stringsAsFactors=F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))

#BH correction
tot.perm$bh=p.adjust(tot.perm$bpval, method="fdr")

#plot qqplot
pdf("/project2/gilad/briana/threeprimeseq/output/plots/qqplot_total_APAperm.pdf") 
qqplot_total= qqplot(-log10(runif(nrow(tot.perm))), -log10(tot.perm$bpval),ylab="-log10 Total permuted pvalue", xlab="Uniform expectation", main="Total permuted pvalues for all snps")
abline(0,1)
dev.off()

#write df with BH  

write.table(tot.perm, file = "/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_Opp/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_permResBH.txt", col.names = T, row.names = F, quote = F)

##nuclear results  


nuc.perm= read.table("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_Opp/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_permRes.txt",head=F, stringsAsFactors=F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
nuc.perm$bh=p.adjust(nuc.perm$bpval, method="fdr")


#plot qqplot
pdf("/project2/gilad/briana/threeprimeseq/output/plots/qqplot_nuclear_APAperm.pdf") 
qqplot(-log10(runif(nrow(nuc.perm))), -log10(nuc.perm$bpval),ylab="-log10 Nuclear permuted pvalue", xlab="Uniform expectation", main="Nuclear permuted pvalues for all snps")
abline(0,1)
dev.off()

# write df with BH
write.table(nuc.perm, file = "/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_Opp/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_permResBH.txt", col.names = T, row.names = F, quote = F)

Write a script to run this:

run_APAqtlpermCorrectQQplot.sh

#!/bin/bash


#SBATCH --job-name=run_APAqtlpermCorrectQQplot
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_APAqtlpermCorrectQQplot.out
#SBATCH --error=run_APAqtlpermCorrectQQplot.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

module load Anaconda3
source activate three-prime-env


Rscript APAqtlpermCorrectQQplot.R

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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.18      digest_0.6.16    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.11    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1