get_Pfam_domain: Function to annotate fusion calls with domain terms

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Function to annotate fusion calls with domain terms

Description

Function to annotate fusion calls with domain terms

Usage

get_Pfam_domain(standardFusioncalls, bioMartDataPfam, keepPartialAnno = FALSE)

Arguments

standardFusioncalls	A dataframe from star fusion or arriba standardized to run through the filtering steps
bioMartDataPfam	A dataframe with gene and domain coordinate information with chromosome_name,gene_start,gene_end,domain_chr,domain_start,domain_end,hgnc_symbol
keepPartialAnno	TRUE or FALSE to keep partial status; defaults to FALSE

Value

Standardized fusion calls as list Gene1A and Gene1B annotated with domain terms and chromosome location; retained and not retained,optionally partially retained

Examples

out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
sfc <- read.delim(out_annofuse)
bioMartDataPfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
domain_list_df <- get_Pfam_domain(standardFusioncalls = sfc, bioMartDataPfam = bioMartDataPfam)

d3b-center/annoFuse documentation built on Feb. 21, 2023, 1:06 a.m.