getAlteredProbes: Get Altered Probes

In gada: Genome Alteration Detection Algorithm (GADA)

Description

This function returns a list with two components. Each component contains a data frame with the name of the probe and the number of individuals who have this probe altered. First component contains such information for gains and second one for losses.

Usage

getAlteredProbes(x, chr, min.perc = 0.1, max.number.cnv = 100, length.base)

Arguments

x	an object of class 'summaryparGADA'
chr	the desired chromosome
min.perc	minimum percentage of individuals that must have a given altered probe. By default is 0.1 (e.g. 10%)
max.number.cnv	maximum number of segments for each individual. The default is 100. If the number of segments for a given individual is larger than 'max.number.cnv' this sample is discarded
length.base	a vector with two components. The first corresponds to the minimum size required to consider a segment as a CNV, while the second one corresponds to the maximum size. If missing, this information is obtained from the attribute 'length.base' of object 'x'

Value

A list with the following components

gains	a data frame containning the name of probes with a gain and the number of individuals who have this probe altered
losses	a data frame containning the name of probes with a loss and the number of individuals who have this probe altered

References

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples", BMC Bioinformatics , Submitted Nov 2009

See Also

parBE, parSBL

Examples

# see vignette

gada documentation built on May 2, 2019, 6:10 p.m.