plotHMMscore: Plot CNV inference score.

Description Usage Arguments Value Examples

View source: R/plotHMMscore_function.R

Description

Plot out CNV inference score. Each row is a sample, each column is a SNP or, exon (WES) or bin (WGS). Red color indicate score favor duplication whereas blue favor deletion.

Usage

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plotHMMscore(icnv_res, h = NULL, t = NULL, title = "score plot",
  output = NULL, col = "")

Arguments

icnv_res

CNV inference result. Result from iCNV_detection() (i.e. iCNV_detection(...))

h

start position of this plot. Default Start of the whole chromosome

t

end position of this plot. Default End of the whole chromosome

title

of this plot. Character value. Type character Default "score plot"

output

generated from output_list_function. If it isn't null, only CNVs in output file will be highlighted. Default NULL

col

Specify if would like to plot in DGV color scheme ('DGV',red for deletion, blue for duplication and grey for diploid) or default color scheme (blue for deletion, red for duplicatin and and green for diploid) Type character. Default ”

Value

void

Examples

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plotHMMscore(icnv_res0,h=21000000, t=22000000, title='my favorite subject')
plotHMMscore(icnv_res0,h=21000000, t=22000000, title='my favorite subject',col='DGV')

zhouzilu/iCNV documentation built on Feb. 16, 2020, 4:53 p.m.