create_gene_level_scna_df: Create Gene-level SCNA Data Frame

In driveR: Prioritizing Cancer Driver Genes Using Genomics Data

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.

driveR documentation built on Aug. 19, 2023, 5:12 p.m.