abs_calling: absCopyNumber calling with user specified parameters

In ShixiangWang/absCopyNumber: Tumor Purity, Ploidy and Absolute Copy Number Estimation

Description

This is the third step for absCopyNumber pipeline, absCopyNumber compute solutions of purity and ploidy, then generate absolute copynumber and (optional) multiplicity for top 1 solution.

Usage

abs_calling(absCopyNumber, samples = NULL, verbose = FALSE)

Arguments

absCopyNumber	a absCopyNumber object generate from abs_prepare function.
samples	character vector to subset samples for calling, default is NULL.
verbose	if TRUE, print extra information.

Value

a absCopyNumber object with calling result.

Author(s)

Shixiang Wang <[e-mail]>

See Also

absCopyNumber, abs_initialize, , abs_prepare

Examples

file_cn = system.file("extdata/example.cn.txt.gz", package = "absCopyNumber")
file_snv = system.file("extdata/example.snv.txt.gz", package = "absCopyNumber")


res1 =  abs_initialize(seg = file_cn, snv = file_snv, verbose = T)
res1 =  abs_prepare(res1)
res1 =  abs_calling(res1, verbose = TRUE)

ShixiangWang/absCopyNumber documentation built on May 28, 2019, 5:42 p.m.