create_gene_level_scna_df {driveR}

Create Gene-level SCNA Data Frame

Description

Create Gene-level SCNA Data Frame

Usage

create_gene_level_scna_df(
  scna_df,
  build = "GRCh37",
  gene_overlap_threshold = 25
)

Arguments

scna_df

the SCNA segments data frame. Must contain:

chr

chromosome the segment is located in

start

start position of the segment

end

end position of the segment

log2ratio

log₂

ratio of the segment

build

genome build for the SCNA segments data frame (default = "GRCh37")

gene_overlap_threshold

the percentage threshold for the overlap between a segment and a transcript (default = 25). This means that if only a segment overlaps a transcript more than this threshold, the transcript is assigned the segment's SCNA event.

Value

data frame of gene-level SCNA events, i.e. table of genes overlapped by SCNA segments.