proteinDomains: # Import protein domains from PROT2HG ———

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

proteinDomains <- data.table::fread(input = '~/prot2hg_1938_112019.csv', sep = ';', stringsAsFactors = FALSE)

Usage

data(proteinDomains)

Format

GRanges containing protein domains and protein-specific sites, derived from PROT2HG (Jan. 2021)

Details

# Select protein-information. proteinDomains <- proteinDomains

# Convert to GRanges. proteinDomains <- GenomicRanges::makeGRangesFromDataFrame(proteinDomains, keep.extra.columns = TRUE, seqnames.field = 'protein_ID', start.field = 'prot_start', end.field = 'prot_end')

# Factorize to reduce size. proteinDomains$type <- factor(proteinDomains$type) proteinDomains$gene <- factor(proteinDomains$gene) proteinDomains$ensembl <- factor(proteinDomains$ensembl)

usethis::use_data(proteinDomains)

Source

proteins

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.