getGenotypeCalls: Extract genotype calls from aroma files

Description Usage Arguments Details Value Author(s) Examples

View source: R/getGenotypeCalls.R

Description

Extract genotype calls from aroma files. It requires to have executed the normalization process suggested by aroma packages, by using signalPreProcess for example.

Usage

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getGenotypeCalls(dataSetName, chromosome, listOfFiles = NULL, verbose = TRUE)

Arguments

dataSetName

The name of the data-set folder (it must correspond to a folder name in rawData folder.)

chromosome

A vector containing the chromosomes for which the genotype call will be extracted.

listOfFiles

A vector containing the names of the files in dataSetName folder for which the genotype signal will be extracted (default is all the files).

verbose

If TRUE print some information (default=TRUE)

Details

The aroma architecture must be respected. The working directory must contain rawData folder and totalAndFracBData folder. To easily access the names of the files available in a dataset, one can use the getListOfFiles function.

Value

a list of length the number of chromosomes containing a data.frame with columns:

chromosome

Chromosome of the signal.

position

Positions associated with the genotype.

genotype

Genotype calls corresponding to selected files; the name of each column is the name of the associated data file name.

featureNames

Names of the probes.

Author(s)

Quentin Grimonprez

Examples

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## Not run: 
#DO NOT EXECUTE before reading the vignette
fracB=getGenotypeCalls("data1",5)

## End(Not run)

MPAgenomics documentation built on March 30, 2021, 5:13 p.m.