Created
August 10, 2024 11:48
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script for filtering a gtex resource from https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/imported/GTEx_V8/ge/
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| #tabix Lung.tsv.gz 1:1-300000000 > lung.chr1.tsv | |
| #tabix Lung.tsv.gz 2:1-300000000 > lung.chr2.tsv | |
| #tabix Lung.tsv.gz 3:1-300000000 > lung.chr3.tsv | |
| #tabix Lung.tsv.gz 4:1-300000000 > lung.chr4.tsv | |
| #tabix Lung.tsv.gz 5:1-300000000 > lung.chr5.tsv | |
| #tabix Lung.tsv.gz 6:1-300000000 > lung.chr6.tsv | |
| #tabix Lung.tsv.gz 7:1-300000000 > lung.chr7.tsv | |
| #tabix Lung.tsv.gz 8:1-300000000 > lung.chr8.tsv | |
| #tabix Lung.tsv.gz 9:1-300000000 > lung.chr9.tsv | |
| #tabix Lung.tsv.gz 10:1-300000000 > lung.chr10.tsv | |
| #tabix Lung.tsv.gz 11:1-300000000 > lung.chr11.tsv | |
| #tabix Lung.tsv.gz 12:1-300000000 > lung.chr12.tsv | |
| #tabix Lung.tsv.gz 13:1-300000000 > lung.chr13.tsv | |
| #tabix Lung.tsv.gz 14:1-300000000 > lung.chr14.tsv | |
| #tabix Lung.tsv.gz 15:1-300000000 > lung.chr15.tsv | |
| #tabix Lung.tsv.gz 16:1-300000000 > lung.chr16.tsv | |
| #tabix Lung.tsv.gz 17:1-300000000 > lung.chr17.tsv | |
| #tabix Lung.tsv.gz 18:1-300000000 > lung.chr18.tsv | |
| #tabix Lung.tsv.gz 19:1-300000000 > lung.chr19.tsv | |
| #tabix Lung.tsv.gz 20:1-300000000 > lung.chr20.tsv | |
| #tabix Lung.tsv.gz 21:1-300000000 > lung.chr21.tsv | |
| #tabix Lung.tsv.gz 22:1-300000000 > lung.chr22.tsv | |
| #tabix Lung.tsv.gz X:1-300000000 > lung.chrX.tsv | |
| nn = c("variant", "r2", "pvalue", "molecular_trait_object_id", "molecular_trait_id", | |
| "maf", "gene_id", "median_tpm", "beta", "se", "an", "ac", "chromosome", | |
| "position", "ref", "alt", "type", "rsid") | |
| library(dplyr) | |
| library(data.table) | |
| chrs = c(1:22, "X") | |
| fn = sprintf("lung.chr%s.tsv", chrs) | |
| filts = lapply(fn, function(x) { | |
| cat(x, "\n") | |
| tmp = fread(x) | |
| names(tmp) = nn | |
| tmp |> dplyr::filter(pvalue < 5e-2) | |
| } | |
| ) | |
| lungpl05 = do.call(rbind, filts) | |
| head(lungpl05) | |
| library(arrow) | |
| write_parquet(lungpl05, "lungpl05.parquet") |
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