readTCGA: Read in tab deliminited file in the TCGA format

Description

Read in tab deliminited file in the TCGA format

Usage

readTCGA(filename, sep = "\t", keyName = "Composite Element REF", Betaname = "Beta_value",
         pData = NULL, array = "IlluminaHumanMethylation450k",
         annotation = .default.450k.annotation, mergeManifest = FALSE,
         showProgress = TRUE)

Arguments

filename

The name of the file to be read from.

sep

The field separator character. Values on each line of the file are separated by this character.

keyName

The column name of the field containing the feature IDs.

Betaname

The character string contained all column names of the beta value fields.

pData

A DataFrame or data.frame describing the samples represented by the columns of mat. If the rownames of the pData don't match the colnames of mat these colnames will be changed. If pData is not supplied, a minimal DataFrame is created.

array

Array name.

annotation

The feature annotation to be used. This includes the location of features thus depends on genome build.

mergeManifest

Should the Manifest be merged to the final object.

showProgress

TRUE displays progress on the console. It is produced in fread's C code.

Value

A GenomicRatioSet object.

Details

This function is a wrapper for makeGenomicRatioSetFromMatrix. It assumes a very specific format, used by TCGA, and then uses the fread function in the data.table package to read the data. To install data.table type install.packages("data.table"). We use this package because the files too large for read.table. Currently, an example of a file that this function reads is here: http://gdac.broadinstitute.org/runs/stddata__2014_10_17/data/UCEC/20141017/gdac.broadinstitute.org_UCEC.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2014101700.0.0.tar.gz. Note it is a 8.1 GB archive.

Examples

Run this code

filename <- "example.txt" ##file must be in the specicif TCGA format
    readTCGA(filename)