gtex_pairs_to_data.frame: import signif_variant_gene_pairs from GTEx to data.frame,...

In vjcitn/tnt4dn8: TnT applications with GWAS in dn8 format

import signif_variant_gene_pairs from GTEx to data.frame, adding symbol and other metadata about genes

Description

import signif_variant_gene_pairs from GTEx to data.frame, adding symbol and other metadata about genes

Usage

gtex_pairs_to_data.frame(pairs_path, gencode_data.frame)

Arguments

pairs_path	character(1), field "gene_id" will be join key
gencode_data.frame	data.frame instance with additional metadata, field "Tx" will be join key

Value

data.frame with pairs records joined with gencode metadata and chr.variant and chr.pos

Note

the variant_id field will be split by underscore and first 2 items are chr and variant position

Examples

pairs_path = system.file("gtex_pairs/lung_demo.pairs.txt.gz", package="tnt4dn8")
data(gencode_26_df)
lit = gtex_pairs_to_data.frame(pairs_path, gencode_26_df)
head(lit)

vjcitn/tnt4dn8 documentation built on Sept. 10, 2022, 11:17 a.m.