readTCGA {minfi} | R Documentation

## 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. Irizarryrafa@jimmy.harvard.edu.

### See Also

`makeGenomicRatioSetFromMatrix`

### Examples

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

    ## End(Not run)

[Package minfi version 1.38.0 Index]