rCGH (version 1.2.2)

readGeneric: Generic rCGH object "rCGH-generic" Constructor

Description

A constructor function which takes a tabulated .txt file as input, possibly in a compressed format (.bz2 or .gz). Notice that precise column names are mandatory, see the details section.

Usage

readGeneric(filePath, sampleName=NA, labName=NA,
    genome = c("hg19", "hg18", "hg38"), verbose=TRUE)

Arguments

filePath

: string. A path to an Generic .txt file.

sampleName

: string. A sample Id. Optional.

labName

: string. A lab Id. Optional.

genome

: string. The genome build to use. Supported genomes are hg18, hg19 (default), and hg38.

verbose

: logical. When TRUE (default), progress is printed.

Value

• An object of class "rCGH"

Details

This generic constructor does not expect any preamble. Mandatory columns are: [object Object],[object Object],[object Object],[object Object]

See Also

readAgilent, readAffySNP6, readAffyCytoScan, setInfo, getInfo

Examples

filePath <- system.file("extdata", "generic.txt.bz2", package = "rCGH")
cgh <- readGeneric(filePath, sampleName = "demo")
cgh