Annotate Driver SSM. — annotate_driver

Retrieve data or use the supplied data frame of genes to get/annotate MAF data indicating which rows are putative driver mutations.

annotate_driver_ssm(
  maf_df,
  lymphoma_type,
  driver_genes,
  noncoding_regions = c(NFKBIZ = "chr3:101578206-101578365", HNRNPH1 =
    "chr5:179,045,946-179,046,683")
)

Arguments

maf_df: Data frame of MAF-format mutations.
lymphoma_type: Optional keyword to find genes for annotation (e.g. "BL","DLBCL","FL") is not specifying driver genes.
driver_genes: Optional vector of Hugo_Symbol of genes for coding mutations.
noncoding_regions: Optional named vector of regions to use to further restrict noncoding mutations per gene.

Value

Incoming MAF, subset to putative driver mutations.

Details

Provide a maf-like data frame with maf_df as the only required parameter. For information on how to use the additional parameters, refer to the parameter descriptions and function examples.

Examples

driver_ssm = annotate_driver_ssm(maf_df = grande_maf,
                                 lymphoma_type = "DLBCL",
                                 noncoding_regions=c("NFKBIZ"="chr3:101578206-101578365"))
#> using 152 genes
#> adding chr3:101578206-101578365 for NFKBIZ
#> [1] 727 125