validatePd:
Validate a sample description file for two-color microarray data
Description
Checks a sample description file describing two-color arrays for proper formatting and if requested guesses column numbers for file names, sample labels and group labels.
Usage
validatePd(pd, fileNameColumn, sampleNameColumn, groupColumn,
ut = "_532.xys", md = "_635.xys")
Arguments
pd
A data frame containing the sample description table
fileNameColumn
Number or name of column containing file names (optional)
sampleNameColumn
Number or name of column containing sample names (optional)
groupColumn
Number or name of column containing group labels (optional)
ut
the file ending that designates untreated channel files
md
the file ending that designates methyl-depleted channel files
Value
If the input data frame is valid: a list containing the fileNameColumn, sampleNameColumn and groupColumn.
If the input data frame is invalid: FALSE
Details
This function checks the formatting of a sample description file to make sure it has suitable columns for file names, sample names and (optionally) group labels. The sample description file should have one line per channel, i.e. two lines per sample corresponding to the red and green channel data files. Values in the sample name column are used to pair the two channels together. If fileNameColumn, sampleNameColumn and/or groupColumn are unspecified a guess will be made.