R/filterForCommonSamples.R

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

#TCGAGeneReport Copyright 2014, 2015, 2016 University of Texas MD Anderson Cancer Center
#
#This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.

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filterForCommonSamples <- function(...)
{
	commonSamples <- NULL
	allNames <- lapply(list(...), function(theData)
	{
		stopifnot(is.matrix(theData))
		substring(colnames(theData), 1, 15)
	})
	for (index in 1:length(allNames))
	{
		if (is.null(commonSamples))
		{
			commonSamples <- allNames[[index]]
		}
		else
		{
			commonSamples <- intersect(commonSamples, allNames[[index]])
		}
	}
	results <- lapply(list(...), function(theDataSet, theCommonList)
	{
		colnames(theDataSet) <- substring(colnames(theDataSet), 1, 15)
		theDataSet[theCommonList]
	}, theCommonList=commonSamples)
	results
}