readGEORawFile {minfi} | R Documentation

## Read in Unmethylated and Methylated signals from a GEO raw file.

### Description

Read in Unmethylated and Methylated signals from a GEO raw file.

### Usage

    readGEORawFile(filename, sep = ",", Uname = "Unmethylated signal",
                   Mname = "Methylated signal", row.names = 1, 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.
`Uname` | A string that uniquely identifies the columns containing the unmethylated signals.
`Mname` | A string that uniquely identifies the columns containing the methylated signals.
`row.names` | The column containing the feature (CpG) IDs.
`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.
`...` | Additional arguments passed to `data.table::fread()`.

### Details

450K experiments uploaded to GEO typically include a raw data file as part of the supplementary materials. Unfortunately there does not appear to be a standard format. This function provides enough flexibility to read these files. Note that you will likely need to change the `sep`, `Uname`, and `Mname` arguments and make sure the first column includes the feature (CpG) IDs. You can use the `readLines` function to decipher how to set these arguments.

Note that the function 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`.

### Value

A GenomicMethylSet object.

### Author(s)

Rafael A. Irizarryrafa@jimmy.harvard.edu.

### See Also

`getGenomicRatioSetFromGEO`

### Examples

    ## Not run:
    library(GEOquery)
    getGEOSuppFiles("GSE29290")
    gunzip("GSE29290/GSE29290_Matrix_Signal.txt.gz")
    # NOTE: This particular example file uses a comma as the decimal separator
    #       (e.g., 0,00 instead of 0.00). We replace all such instances using the
    #       command line tool 'sed' before reading in the modified file.
    cmd <- paste0("sed s/,/\./g GSE29290/GSE29290_Matrix_Signal.txt > ",
                  "GSE29290/GSE29290_Matrix_Signal_mod.txt")
    system(cmd)
    gmset <- readGEORawFile(filename = "GSE29290/GSE29290_Matrix_Signal_mod.txt",
                            Uname = "Signal_A",
                            Mname = "Signal_B",
                            sep = "\t")

    ## End(Not run)

[Package minfi version 1.40.0 Index]