validatePd: Validate a sample description file for two-color microarray...

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

View source: R/charm.R

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

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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

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.

Value

If the input data frame is valid: a list containing the fileNameColumn, sampleNameColumn and groupColumn. If the input data frame is invalid: FALSE

Author(s)

Martin Aryee <[email protected]>

See Also

readCharm

Examples

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# See dmrFdr

Bioconductor-mirror/charm documentation built on June 1, 2017, 5:29 a.m.