caai: Complex arm-wise aberration index (CAAI)

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

Description

Computes complex arm-wise aberration index (CAAI) for a chromosome arm. CAAI is an indicator of complex rearrangements. See Russnes et al (DOI: 10.1126/scitranslmed.3000611) for a detailed definition.

Usage

caai(seg_values, seg_start, seg_end, alpha = 10000/0.005, thetaH = 1.2,
  R = 2e+07)

Arguments

seg_values	Numeric vector, with mean (or other measure) of log ratio for each segment on chromosome arm.
seg_start	Numeric vector, with genomic position of segment start.
seg_end	Numeric vector, with genomic position of segment end.
alpha	A number, alpha value for computation of P. Defaults to the value used by Russnes et al.
thetaH	A number, theta value for compuation of Q. Defaults to the value used by Russnes et al.
R	A number, size of window R over which to sum S. Defaults to the value used by Russnes et al.

Value

Complex arm-wise aberration 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[,.(caai = caai(mean, start.pos, end.pos)), by=.(chrom, arm)]

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