| Title: | Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project |
|---|---|
| Description: | Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. |
| Authors: | Malgorzata Nowicka [aut, cre] |
| Maintainer: | Malgorzata Nowicka <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.40.0 |
| Built: | 2026-10-10 11:10:48 UTC |
| Source: | https://git.bioconductor.org/packages/GeuvadisTranscriptExpr |
Subsets of raw data available in this package and saved as Rdata objects for faster loading.
counts gene_ranges genotypes snp_rangescounts gene_ranges genotypes snp_ranges
counts is a data frame with subset of counts from TrQuantCount_CEU_chr19.tsv
gene_ranges is a GRanges object containing subset of gene coordinates from genes_chr19.bed
genotypes is a data frame with subset of genotypes from genotypes_CEU_chr19.tsv
snp_ranges is a Granges object containing subset of SNP coordinates from genotypes_CEU_chr19.tsv
For all the details on how these data sets were produced, see examples.
counts, gene_ranges, genotypes, snp_ranges
Lappalainen T, Sammeth M, Friedlander MR, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501(7468):506-11
library(rtracklayer) data_dir <- system.file("extdata", package = "GeuvadisTranscriptExpr") gene_id_subset <- readLines(file.path(data_dir, "gene_id_subset.txt")) snp_id_subset <- readLines(file.path(data_dir, "snp_id_subset.txt")) # Load gene ranges with names! gene_ranges <- import(file.path(data_dir, "genes_chr19.bed")) names(gene_ranges) <- mcols(gene_ranges)$name gene_ranges <- gene_ranges[gene_id_subset, ] # Load transcript counts counts <- read.table(file.path(data_dir, "TrQuantCount_CEU_chr19.tsv"), header = TRUE, sep = "\t", as.is = TRUE) counts <- counts[counts$Gene_Symbol %in% gene_id_subset, ] # Load genotypes genotypes <- read.table(file.path(data_dir, "genotypes_CEU_chr19.tsv"), header = TRUE, sep = "\t", as.is = TRUE) genotypes <- genotypes[genotypes$snpId %in% snp_id_subset, ] # Create SNP ranges with names! snp_ranges <- GRanges(Rle(genotypes$chr), IRanges(genotypes$start, genotypes$end)) names(snp_ranges) <- genotypes$snpIdlibrary(rtracklayer) data_dir <- system.file("extdata", package = "GeuvadisTranscriptExpr") gene_id_subset <- readLines(file.path(data_dir, "gene_id_subset.txt")) snp_id_subset <- readLines(file.path(data_dir, "snp_id_subset.txt")) # Load gene ranges with names! gene_ranges <- import(file.path(data_dir, "genes_chr19.bed")) names(gene_ranges) <- mcols(gene_ranges)$name gene_ranges <- gene_ranges[gene_id_subset, ] # Load transcript counts counts <- read.table(file.path(data_dir, "TrQuantCount_CEU_chr19.tsv"), header = TRUE, sep = "\t", as.is = TRUE) counts <- counts[counts$Gene_Symbol %in% gene_id_subset, ] # Load genotypes genotypes <- read.table(file.path(data_dir, "genotypes_CEU_chr19.tsv"), header = TRUE, sep = "\t", as.is = TRUE) genotypes <- genotypes[genotypes$snpId %in% snp_id_subset, ] # Create SNP ranges with names! snp_ranges <- GRanges(Rle(genotypes$chr), IRanges(genotypes$start, genotypes$end)) names(snp_ranges) <- genotypes$snpId