Results from e-QTL

by Brain region

work_results = "~/pd-omics/katia/Microglia/mic_314s/eQTL_mic/2nd_pass_eQTL/EUR/QTL-mapping-pipeline/results/"
work_dir = "~/pd-omics/katia/scripts/GitHub_scripts/glia_omics/2nd_pass_mic_314s/QTL_pages/2nd_pass/eQTL_lists_symbol_2nd/"

## Get conversion table for Gencode 30
gencode_30 = read.table("~/pd-omics/katia/ens.geneid.gencode.v30")
colnames(gencode_30) = c("ensembl","symbol")

MFG eGenes qvalue 10%

Media Frontal Gyrus - PEER 10. Number of eGenes:

peer10 = read.table(gzfile(paste0(work_results, "MFG_eur_expression/peer10/MFG_eur_expression_peer10.cis_qtl.txt.gz")), stringsAsFactors=F, header = T)
rownames(peer10) = peer10$phenotype_id
sum(peer10$qval < 0.10) 

[1] 267

eGenes = peer10[(peer10$qval < 0.10),]
eGenes = merge(eGenes, gencode_30, by.x = "phenotype_id", by.y = "ensembl")
write.table(eGenes, file = paste0(work_dir, "eGEnes_eur_MFG_qval10per.txt"), sep = "\t", quote = F, row.names = F)

MFG_symbol = unique(eGenes$symbol)
createDT(eGenes[, c("symbol", colnames(eGenes)[!colnames(eGenes)=="symbol"])])

STG eGenes qvalue 10%

Superior Temporal Gyrus - PEER 10. Number of eGenes:

peer10 = read.table(gzfile(paste0(work_results, "STG_eur_expression/peer10/STG_eur_expression_peer10.cis_qtl.txt.gz")), stringsAsFactors=F, header = T)
rownames(peer10) = peer10$phenotype_id
sum(peer10$qval < 0.10) 

[1] 154

eGenes = peer10[(peer10$qval < 0.10),]
eGenes = merge(eGenes, gencode_30, by.x = "phenotype_id", by.y = "ensembl")
write.table(eGenes, file = paste0(work_dir, "eGEnes_eur_STG_qval10per.txt"), sep = "\t", quote = F, row.names = F)

STG_symbol = unique(eGenes$symbol)
createDT(eGenes[, c("symbol", colnames(eGenes)[!colnames(eGenes)=="symbol"])])

THA eGenes qvalue 10%

Thalamus - PEER 10. Number of eGenes:

peer10 = read.table(gzfile(paste0(work_results, "THA_eur_expression/peer10/THA_eur_expression_peer10.cis_qtl.txt.gz")), stringsAsFactors=F, header = T)
rownames(peer10) = peer10$phenotype_id
sum(peer10$qval < 0.10) 

[1] 196

eGenes = peer10[(peer10$qval < 0.10),]
eGenes = merge(eGenes, gencode_30, by.x = "phenotype_id", by.y = "ensembl")
write.table(eGenes, file = paste0(work_dir, "eGEnes_eur_THA_qval10per.txt"), sep = "\t", quote = F, row.names = F)

THA_symbol = unique(eGenes$symbol)
createDT(eGenes[, c("symbol", colnames(eGenes)[!colnames(eGenes)=="symbol"])])

SVZ eGenes qvalue 10%

Subventricular zone - PEER 5. Number of eGenes:

peer5 = read.table(gzfile(paste0(work_results, "SVZ_eur_expression/peer5/SVZ_eur_expression_peer5.cis_qtl.txt.gz")), stringsAsFactors=F, header = T)
rownames(peer5) = peer5$phenotype_id
sum(peer5$qval < 0.10) 

[1] 94

eGenes = peer5[(peer5$qval < 0.10),]
eGenes = merge(eGenes, gencode_30, by.x = "phenotype_id", by.y = "ensembl")
write.table(eGenes, file = paste0(work_dir, "eGEnes_eur_SVZ_qval10per.txt"), sep = "\t", quote = F, row.names = F)

SVZ_symbol = unique(eGenes$symbol)
createDT(eGenes[, c("symbol", colnames(eGenes)[!colnames(eGenes)=="symbol"])])

eGenes overlap

Considering only the symbol.

sample_overlap = list(MFG = MFG_symbol,
                      STG = STG_symbol,
                      THA = THA_symbol,
                      SVZ = SVZ_symbol)

venn(sample_overlap, zcolor = pal_lancet(palette = c("lanonc"), alpha = 1)(5), 
     cexil = 1.1, ilcs = 1.5, sncs = 1.0, lwd = 1)

sessionInfo()

R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.4

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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

other attached packages: [1] venn_1.8 ggsci_2.9 ggplot2_3.3.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.4 later_1.0.0 pillar_1.4.3 compiler_3.6.1
[5] tools_3.6.1 digest_0.6.25 jsonlite_1.6.1 evaluate_0.14
[9] lifecycle_0.2.0 tibble_2.1.3 gtable_0.3.0 pkgconfig_2.0.3
[13] rlang_0.4.5 shiny_1.4.0 crosstalk_1.0.0 yaml_2.2.0
[17] xfun_0.11 fastmap_1.0.1 withr_2.1.2 dplyr_0.8.5
[21] stringr_1.4.0 knitr_1.26 admisc_0.5 htmlwidgets_1.5.1 [25] grid_3.6.1 DT_0.13 tidyselect_0.2.5 glue_1.4.0
[29] R6_2.4.1 rmarkdown_2.0 purrr_0.3.3 magrittr_1.5
[33] promises_1.1.0 scales_1.1.0 htmltools_0.4.0 assertthat_0.2.1 [37] xtable_1.8-4 mime_0.8 colorspace_1.4-1 httpuv_1.5.2
[41] stringi_1.4.6 munsell_0.5.0 crayon_1.3.4