Last updated: 2019-09-06

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Knit directory: apaQTL/analysis/

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Unstaged changes:
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Modified:   code/SnakefilefiltPAS
    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
    Modified:   data/MetaDataSequencing.txt
    Modified:   docs/figure/DiffIsoAnalysis.Rmd/figure1Emain-1.pdf
    Modified:   docs/figure/DiffIsoAnalysis.Rmd/figure1Esubset-1.pdf
    Modified:   docs/figure/chromHHMQTL.Rmd/figure3D-1.pdf
    Modified:   docs/figure/exvunexpeQTL.Rmd/figure3C-1.pdf
    Modified:   docs/figure/pQTLandeQTLoverlap.Rmd/figure3A-1.pdf
    Modified:   docs/figure/propeQTLs_explained.Rmd/figure3B-1.pdf
    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
html d3fbe36 brimittleman 2019-08-08 Build site.
Rmd 85059ca brimittleman 2019-08-08 add ld snps
html 33a700a brimittleman 2019-07-25 Build site.
Rmd f3e3e16 brimittleman 2019-07-25 small edits from paper writing and add gwas analysis

https://brimittleman.github.io/threeprimeseq/apaQTLoverlapGWAS.html

https://brimittleman.github.io/threeprimeseq/OverlapFullGWASCatelog.html

Nuclear qtls: ../data/apaQTLs/NuclearQTLSNPsRSID.txt Total qtls: ../data/apaQTLs/TotalQTLSNPsRSID.txt

require(tidyverse)
Loading required package: 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()
mkdir  ../data/GWAS_overlap/
mkdir ../data/GWAS_overlap/TotalApaQTL_LD/
mkdir  ../data/GWAS_overlap/NuclearApaQTL_LD/
#sbatch LD_qtl.sh
python nucQTLGWAS.py
results=read.table("../data/GWAS_overlap/NuclearSNPinGWAS.txt",header = F, stringsAsFactors = F,sep="\t")


resultsSNPs=results %>% select(V5) %>% unique()

Check examples:

1311 chr5 95242930 95242931 rs56219066 26007630 Swaminathan B 2015-05-26 Nat Commun Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma. Multiple myeloma and monoclonal gammopathy 2,194 European ancestry multiple myeloma cases, 251 European ancestry monoclonal gammopathy cases, 294,390 European ancestry controls 586 European ancestry multiple myeloma cases, 2,111 European ancestry controls 5q15 ELL2 rs56219066-T 0.711 2E-10 1.24 [1.16-1.33] Illumina [12100000] (imputed) N ELL2 intron + peak106823 rs56219066

1536 chr10 124693586 124693587 rs7904973 30275531 Klarin D 2018-10-01 Nat Genet Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program. LDL cholesterol 215,551 European ancestry individuals, 57,332 African American individuals, 24,743 Hispanic individuals Up to 319,677 individuals 10q26.13 C10orf88 rs7904973-T 0.5573 1E-14 0.0203 [0.015-0.025] mg dl-1 increase Affymetrix [up to 31400000] (imputed) N

C10orf88 intron + peak19881 rs7904973

Full catelog: Get snps in LD using the https://ldlink.nci.nih.gov/#ldproxy-tab. Run this with through command line. To output code for each snp:

sbatch LD_snpsproxy.sh

Run each line independently Concatinate all results filter for r2 >.9

sbatch run_filtersnpLD.sh

Concatinate this with the RSID for the astual QTLS

cat /project2/gilad/briana/apaQTL/data/apaQTLs/LDsnps_9/* ../data/apaQTLs/NuclearQTLSNPsRSID.txt  > /project2/gilad/briana/apaQTL/data/apaQTLs/NuclearQTLSNPsRSID_withLD.txt

../data/apaQTLs/NuclearQTLSNPsRSID_withLD.txt

python nucQTLGWAS_withLD.py
cut -f 5 ../data/GWAS_overlap/NuclearSNPinGWAS_withLD.txt | sort | uniq | wc -l

#105

105 overlaps of 544 snps

105/544
[1] 0.1930147

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