Run molecular QTLs

Last updated: 2019-08-30

Checks: 6 1

Knit directory: apaQTL/analysis/

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Unstaged changes:
    Modified:   analysis/NuclearSpecAPAqtl.Rmd
    Modified:   analysis/PAS_graphs.Rmd
    Modified:   analysis/PrematureTermQTL.Rmd
    Modified:   analysis/compareAnnotatedpas.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/rerunQTL_changePC.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_Nominal.sh
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/bam2bw.sh
    Modified:   code/bed2saf.py
    Modified:   code/cluster.json
    Modified:   code/clusterfiltPAS.json
    Modified:   code/config.yaml
    Modified:   code/environment.yaml
    Modified:   code/makePheno.py
    Modified:   code/mergeAllBam.sh
    Modified:   code/mergeByFracBam.sh
    Modified:   code/mergePeaks.sh
    Modified:   code/peakFC.sh
    Modified:   code/snakemake.batch
    Modified:   code/snakemakePAS.batch
    Modified:   code/snakemakefiltPAS.batch
    Modified:   code/submit-snakemake.sh
    Modified:   code/submit-snakemakePAS.sh
    Modified:   code/submit-snakemakefiltPAS.sh
    Deleted:    code/test.txt
    Deleted:    reads_graphs.Rmd

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	80f8466	brimittleman	2019-08-30	add riboQTL and fix expression name switch
html	33a700a	brimittleman	2019-07-25	Build site.
Rmd	f3e3e16	brimittleman	2019-07-25	small edits from paper writing and add gwas analysis
html	cd60f50	brimittleman	2019-06-20	Build site.
Rmd	6df08b6	brimittleman	2019-06-20	change analysis to include not tested in total as nuc spec
html	2b8bf0c	brimittleman	2019-06-17	Build site.
Rmd	54946d7	brimittleman	2019-06-17	add mol qtl code

I will rerun the eQTLs and pQTLs to overlap effect sizes with my data. These were downloaded from Li et al 2016 and processed in https://brimittleman.github.io/threeprimeseq/.

library(tidyverse)

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

✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.3.1  
✔ readr   1.3.1       ✔ forcats 0.3.0

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

I will move the sample, pca, and phenotpye files to the apaQTL dir.

mkdir ../data/molPhenos/
mkdir ../data/molQTLs/
sbatch EandPqtls.sh

Concatinate the results:

cat ../data/molQTLs/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.chunk* > ../data/molQTLs/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.AllNomRes.txt


cat ../data/molQTLs/fastqtl_qqnorm_prot.fixed.nominal.chunk* > ../data/molQTLs/fastqtl_qqnorm_prot.fixed.nominal.AllNomRes.txt

Fix gene names in the results:

python changenomQTLres2geneName.py

How many genes are tested in nuclear apa and protein and expression

permProt=read.table("../data/molQTLs/fastqtl_qqnorm_prot.fixed.perm.AllNomRes.GeneName.txt", header = F, stringsAsFactors = F,col.names=c("Gene", "nvar", "shape1", "shape2", "dummy", "rsid", "dist", "nom", "slope", "perm1", "bpval"))

permEx=read.table("../data/molQTLs/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.AllNomRes.GeneName.txt", header = F, stringsAsFactors = F,col.names=c("Gene", "nvar", "shape1", "shape2", "dummy", "rsid", "dist", "nom", "slope", "perm1", "bpval")) %>% select(Gene)

nuclearperm=read.table("../data/apaQTLPermuted_4pc/APApeak_Phenotype_GeneLocAnno.Nuclear_permResBH.txt",stringsAsFactors = F, header = T) %>% separate(pid, into=c("chr", "start", "end", "geneID"),sep=":") %>% separate(geneID, into=c("Gene", "loc", "strand", "PAS"), sep="_") %>% select(Gene) %>% unique()

permProt %>% inner_join(nuclearperm, by="Gene") %>% inner_join(permEx, by="Gene") %>% nrow()

[1] 1549

ribo data

I also want to look at ribo data so I need to call QTLs with these as well.

sbatch riboQTL.sh

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] forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1   purrr_0.3.2    
[5] readr_1.3.1     tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.1  
[9] tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       cellranger_1.1.0 plyr_1.8.4       compiler_3.5.1  
 [5] pillar_1.3.1     git2r_0.25.2     highr_0.7        workflowr_1.4.0 
 [9] tools_3.5.1      digest_0.6.18    lubridate_1.7.4  jsonlite_1.6    
[13] evaluate_0.12    nlme_3.1-137     gtable_0.2.0     lattice_0.20-38 
[17] pkgconfig_2.0.2  rlang_0.4.0      cli_1.1.0        rstudioapi_0.10 
[21] yaml_2.2.0       haven_1.1.2      withr_2.1.2      xml2_1.2.0      
[25] httr_1.3.1       knitr_1.20       hms_0.4.2        generics_0.0.2  
[29] fs_1.3.1         rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5
[33] glue_1.3.0       R6_2.3.0         readxl_1.1.0     rmarkdown_1.10  
[37] modelr_0.1.2     magrittr_1.5     whisker_0.3-2    backports_1.1.2 
[41] scales_1.0.0     htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0
[45] colorspace_1.3-2 stringi_1.2.4    lazyeval_0.2.1   munsell_0.5.0   
[49] broom_0.5.1      crayon_1.3.4

Run molecular QTLs

Briana Mittleman

6/17/2019

ribo data