plotindi: Individual sample plot

In zhouzilu/iCNV: Integrated Copy Number Variation detection

Description

Plot relationship between platforms and features for each individual. Only work for muli-platform inference.

Usage

plotindi(ngs_plr, snp_lrr, ngs_baf, snp_baf, ngs_plr.pos, snp_lrr.pos,
  ngs_baf.pos, snp_baf.pos, icnvres, I = numeric(), h = NULL, t = NULL)

Arguments

ngs_plr	A list of NGS intensity data. Each entry is an individual. If no NGS data, no need to specify.
snp_lrr	A list of SNP array intensity data. Each entry is an individual. If no SNP array data, no need to specify.
ngs_baf	A list of NGS BAF data. Each entry is an individual. If no NGS data, no need to specify.
snp_baf	A list of SNP array BAF data. Each entry is an individual. If no SNP array data, no need to specify.
ngs_plr.pos	A list of NGS intensity postion data. Each entry is an individual with dimension= (#of bins or exons, 2(start and end position)). If no NGS data, no need to specify.
snp_lrr.pos	A list of SNP array intensity postion data. Each entry is an individual with length=#of SNPs. If no SNP array data, no need to specify.
ngs_baf.pos	A list of NGS BAF postion data. Each entry is an individual with length=#of BAFs. If no NGS data, no need to specify.
snp_baf.pos	A list of SNP array BAF postion data. Each entry is an individual with length=#of BAFs. If no SNP array data, no need to specify.
icnvres	CNV inference result. The output from iCNV_detection()
I	Indicating the position of the individual to plot. Type integer.
h	start position of this plot. Default Start of the whole chromosome
t	end position of this plot. Default End of the whole chromosome

Value

void

Examples

plotindi(ngs_plr,snp_lrr,ngs_baf,snp_baf,
 ngs_plr.pos,snp_lrr.pos,ngs_baf.pos,snp_baf.pos,
 icnv_res0,I=1)

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