RunCNV: RunCNV

In findlaycopley/PlotCNV: Plot a pretty copynumber plot

RunCNV

Description

Run the whole pipeline start to finish This function will take a dataframe with sample, chr, start.pos, end.pos and call. It will create an instance of the CNVvault class Then it will order this class based on the total amount of the geneome editted. Then it will generate the positions for each sample on the y-axis Then it will plot the output

Usage

RunCNV(Copynumber, ...)

Arguments

Copynumber	Dataframe of your segments. REQUIRED
genome	The genome to use for plotting. Currently only works on hg19. Default: "hg19"
chr	string: name of the column for the chromosome. Default: "chr"
sampleID	string: name of the column for the sample IDs. Default: "sampleID"
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"

Examples

CNV <- generateTestData()
RunCNV(CNV)
## If you have differnet column names specify them when calling the function
RunCNV(CNV, chr="CHROM","start.pos" = "Start", sampleID="sample")

## You can run the functions seperately too:
CNV <- prepareCNV(Copynumber, chr=chr, sampleID=sampleID, start.pos=start.pos, end.pos=end.pos, calls=calls)
CNV <- orderCNV(ReturnClass)
CNV <- setPositionsCNV(ReturnClass, genome=genome)
CNV <- plotCopynumber(ReturnClass)

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