Last updated: 2019-06-25

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Knit directory: apaQTL/analysis/

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Rmd 3e288f8 brimittleman 2019-06-25 add tf analysis

library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
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✔ readr   1.3.1       ✔ forcats 0.3.0  
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(workflowr)
This is workflowr version 1.3.0
Run ?workflowr for help getting started

I want to understand what mechanisms could be driving the apaQTLs. T odo this I am going to look for TF motifs that are enriched for disruption in the apaQTLs. I am using https://ccg.epfl.ch/snp2tfbs/pwmviewer.php and am giving it the list of uniq rsids for the apaQTLs.

Total:

total_tf=read.table("../data/TF_motifdisruption/TotalTFenrich_output_27069.txt", stringsAsFactors = F, col.names = c("name", "genomeMatches","setMatches", "fractionHits", "enrichment","pval"))
total_tf_sig=total_tf %>% filter(pval<.05)
total_matches=read.table("../data/TF_motifdisruption/TotalTFmatchesAnn_output_27069.txt", stringsAsFactors = F,col.names = c("chr", "pos", "ref", "alt", "loc","gene", "score1", "score2", "snp", "TF"))
total_matches_sig=total_matches %>% filter(TF %in% total_tf_sig$name)
ggplot(total_matches_sig, aes(x=TF,fill=loc)) + geom_bar()+ labs(y="Number of SNP", title="Location of Enriched TF motifs \n Total apaQTLs")

Nuclear

nuclear_tf=read.table("../data/TF_motifdisruption/NuclearTFenrich_output_25094.txt", stringsAsFactors = F, col.names = c("name", "genomeMatches","setMatches", "fractionHits", "enrichment","pval"))
nuclear_tf_sig=nuclear_tf %>% filter(pval<.05)
nuclear_matches=read.table("../data/TF_motifdisruption/NuclearTFmatchesAnn_output_25094.txt", stringsAsFactors = F,col.names = c("chr", "pos", "ref", "alt", "loc","gene", "score1", "score2", "snp", "TF"))
nuclear_matches_sig=nuclear_matches %>% filter(TF %in% nuclear_tf_sig$name)
ggplot(nuclear_matches_sig, aes(x=TF,fill=loc)) + geom_bar()+theme(axis.text.x = element_text(angle = 90, hjust = 1)) +labs(y="Number of SNP", title="Location of Enriched TF motifs \n Nuclear apaQTLs")


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] workflowr_1.3.0 forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1  
 [5] purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.1   
 [9] ggplot2_3.1.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       cellranger_1.1.0 pillar_1.3.1     compiler_3.5.1  
 [5] git2r_0.25.2     plyr_1.8.4       tools_3.5.1      digest_0.6.18   
 [9] lubridate_1.7.4  jsonlite_1.6     evaluate_0.12    nlme_3.1-137    
[13] gtable_0.2.0     lattice_0.20-38  pkgconfig_2.0.2  rlang_0.3.1     
[17] cli_1.0.1        rstudioapi_0.10  yaml_2.2.0       haven_1.1.2     
[21] withr_2.1.2      xml2_1.2.0       httr_1.3.1       knitr_1.20      
[25] hms_0.4.2        generics_0.0.2   fs_1.2.6         rprojroot_1.3-2 
[29] grid_3.5.1       tidyselect_0.2.5 glue_1.3.0       R6_2.3.0        
[33] readxl_1.1.0     rmarkdown_1.10   modelr_0.1.2     magrittr_1.5    
[37] whisker_0.3-2    backports_1.1.2  scales_1.0.0     htmltools_0.3.6 
[41] rvest_0.3.2      assertthat_0.2.0 colorspace_1.3-2 labeling_0.3    
[45] stringi_1.2.4    lazyeval_0.2.1   munsell_0.5.0    broom_0.5.1     
[49] crayon_1.3.4