readTCGA: Read in tab deliminited file in the TCGA format

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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.

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.

Value

A GenomicRatioSet object.

Author(s)

Rafael A. [e-mail].

See Also

makeGenomicRatioSetFromMatrix

Examples

## Not run: 
    filename <- "example.txt" ##file must be in the specicif TCGA format
    readTCGA(filename)

## End(Not run)

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.