prepareCNV: prepareCNV

In findlaycopley/PlotCNV: Plot a pretty copynumber plot

prepareCNV

Description

Process data for copynumber plot

Usage

prepareCNV(
  Copynumber,
  sampleID = "sampleID",
  genome = "hg19",
  chr = "chr",
  start.pos = "start.pos",
  end.pos = "end.pos",
  calls = "calls",
  ...
)

Arguments

Copynumber	Dataframe of your segments. REQUIRED
sampleID	string: name of the column for the sample IDs. Default: "sampleID"
genome	string. The geneome to download from UCSC. Default: hg19
chr	string: name of the column for the chromosome. Default: "chr"
start.pos	string: name of the column for the start positions of the segments. Default: "start.pos"
end.pos	string: name of the column for the end positions of the segments. Default: "end.pos"
calls	string: name of the column for the SV type of the segments. Default: "calls"
FinalChrom	string. The final chromosome to include in the plot. Default: chrX

Details

This function will take a dataframe with sample, chr, start.pos, end.pos and call. It will create an instance of the CNVvault class

Examples

prepareCNV()

findlaycopley/PlotCNV documentation built on Feb. 27, 2025, 1:55 a.m.