getChromosomeDat: Cromosome CNV Data

In gada: Genome Alteration Detection Algorithm (GADA)

Description

Obtains a matix of CNV segments and subject samples, from segmentation output

Usage

getChromosomeDat(object, ch, gg, verbose = TRUE)

Arguments

object	concatenated list containing segmentation outcome for each subject, chromosome and population.
ch	chromosome number.
gg	genetic info: data.frame with probe names, chromosome number and genomic positions of each CNV.
verbose	whether to print detailed progress on R prompt.

Details

For object, concatenation by subject and chromosome, within a single population, is readily provided by the function summary.parGADA on an object parGADA that has been previously segemnted. Population concatenation is the result of c(summary{parGADA1}), summary{parGADA2}), ... across groups.

Value

returns a matrix with segment calling (-1:loss,0:nochange,1:gain) for each probe across the whole subject sample.

See Also

reduceMatrix

Examples

## Not run: 

# 'HapMap270Cnv.RData' file can be downloaded from ...

load("Hapmap270Cnv.RData")

ch<-6
mat<-get.chromosome.dat(segments,ch,gen.info)
dim(mat)
mat[1:5,1:5]

## End(Not run)

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