Create Gene-level SCNA Data Frame

Source: R/utility.R

Create Gene-level SCNA Data Frame

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

Arguments

scna_segs_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.