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:

ProbeName:: Character strings. Typicaly the probe ids.
ChrNum:: numeric. The chromosome numbers. In case Chr X and Y are used and named as "X" and "Y", these notations will be converted into 23 and 24, respectively.
ChrStart:: numeric. The chromosomal probes locations.
Log2Ratio:: numeric. The corresponding Log2Ratios.

Examples

Run this code


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

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