readGeneric: Generic rCGH object '"rCGH-generic"' Constructor

In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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"), ploidy = 2, 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.
ploidy	: numeric. A priori ploidy value, when known, to adjust the estimation of copy numbers. Default is 2.
verbose	: logical. When TRUE (default), progress is printed.

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.

Value

An object of class "rCGH"

Author(s)

Frederic Commo

See Also

readAgilent, readAffySNP6, readAffyCytoScan, readAffyOncoScan, setInfo, getInfo

Examples

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

rCGH documentation built on Nov. 8, 2020, 8:30 p.m.