waai: Whole-arm aberration index (WAAI)

In arnijohnsen/arjtools: Collection of tools used in copy number variation analysis

Description

Computes whole-arm aberration index (WAAI) for a chromosome arm. WAAI is an indicator of whole-arm gains and losses. See Russnes et al (DOI: 10.1126/scitranslmed.3000611) for a detailed definition.

Usage

waai(seg_values, seg_nprobes)

Arguments

seg_values	Numeric vector, with mean (or other measure) of log ratio for each segment on chromosome arm.
seg_nprobes	Numeric vector, with number of probes in each segment.

Value

Whole-arm abberation index for the given chromosome arm.

Examples

# Read aCGH data to data.frame dat
seg <- copynumber::pcf(dat)
seg.dt <- data.table::data.table(seg)
seg.dt[,.(waai = waai(mean, n.probes)), by=.(chrom, arm)]

arnijohnsen/arjtools documentation built on May 10, 2019, 1:45 p.m.