fusion_driver: Filter standardized fusion calls for driver fusions

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

Filter standardized fusion calls for driver fusions

Description

If standardized fusion calls are annotated using the geneListReferenceDataTab and fusionReferenceDataTab filters out fusion calls where partner genes are not annotated. If standardized fusion is not annotated it will be annotated with geneListReferenceDataTab and fusionReferenceDataTab provided. Domain retention status for Gene1A and Gene1B for the given pfamIDs is also annotated; defaults to kinase domain retention status information

Usage

fusion_driver(
  standardFusioncalls,
  filterPutativeDriver = TRUE,
  annotated = TRUE,
  geneListReferenceDataTab,
  fusionReferenceDataTab,
  checkDomainStatus = FALSE,
  domainsToCheck
)

Arguments

standardFusioncalls	A dataframe from star fusion or arriba (more callers to be added)
filterPutativeDriver	filter out fusion calls where partner genes are not annotated from with gene and fusion reference list by annnoFuse::annotate_fusion_calls()
annotated	Logical value to specify if input if annotated by annnoFuse::annotate_fusion_calls()
geneListReferenceDataTab	A dataframe with column 1 as GeneName 2 source file 3 type; collapse to summarize type
fusionReferenceDataTab	A dataframe with column 1 as FusionName 2 source file 3 type; collapse to summarize type
checkDomainStatus	Logical value to check if domain status in fused gene for given domansToCheck, default to FALSE
domainsToCheck	pfamID to check for retention status, the IDs can be found here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/pfamDesc.txt.gz, defaults to using kinase pfam IDs since the fusions with kinase domain are more relevant for therapy

Value

Putative Driver standardized fusion calls annotated with gene list and fusion list provided in reference folder. If checkDomainStatus == TRUE and domain retention status for given pfamID is also provided along with the gene location corresponding to the domain retention status

Examples

out_annofuse <-
  system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
sfc <- read.delim(out_annofuse)
geneListReferenceDataTab <- read.delim(
  system.file("extdata", "genelistreference.txt", package = "annoFuseData"),
  stringsAsFactors = FALSE
)
fusionReferenceDataTab <- read.delim(
  system.file("extdata", "fusionreference.txt", package = "annoFuseData"),
  stringsAsFactors = FALSE
)

bioMartDataPfam <-
  readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
kinaseid <- unique(bioMartDataPfam$pfam_id[grep("kinase", bioMartDataPfam$NAME)])
fusion_driver_df <- fusion_driver(sfc,
  annotated = TRUE,
  geneListReferenceDataTab = geneListReferenceDataTab,
  fusionReferenceDataTab = fusionReferenceDataTab,
  checkDomainStatus = FALSE,
  domainsToCheck = kinaseid
)

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