getCounts: Number of CNVs per sample

In isglobal-brge/R-GADA: Genome Alteration Detection Algorithm (GADA)

Description

This function summarize the number of samples that are having an alteration in a given genomic region

Usage

getCounts(x, group, id="sample")

Arguments

x	an object of class 'GRanges' obtained after applying 'getCNVs' function
group	the name of the grouping variable available in the object 'x'
id	the name of the variable having sample id. The default is 'sample'

Value

This function returns a list having two elements. The first element, called 'counts', contains the number of samples of each segment by the variable 'group'. The second element, called 'n', contains the total number of CNVs by 'group' variable.

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, 2010;11:380.

See Also

parSBL, setupParGADA, parBE

Examples

 ## Not run: 
  See the vignette
 
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isglobal-brge/R-GADA documentation built on May 24, 2019, 5:03 a.m.