readGEORawFile: Read in Unmethylated and Methylated signals from a GEO raw...
In minfi: Analyze Illumina Infinium DNA methylation arrays

Description Usage Arguments Details Value Author(s) See Also Examples

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

readGEORawFile(filename, sep = ",", Uname = "Unmethylated signal",
               Mname = "Methylated signal", row.names = 1, pData = NULL,
               array = "IlluminaHumanMethylation450k",
               annotation = .default.450k.annotation, mergeManifest = FALSE,
               showProgress = TRUE, ...)

`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()`.

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.

A GenomicMethylSet object.

Rafael A. Irizarryrafa@jimmy.harvard.edu.

getGenomicRatioSetFromGEO

## 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)