getPlotSummaryData {caOmicsV} | R Documentation |
Extract required rows and columns from a summary data set.
getPlotSummaryData(summaryData, sampleNames=NULL, geneNames=NULL)
summaryData |
a data frame with summary data for each gene (rows are for genes and columns are summary values) or for each sample (rows are summary values and columns are sample names) |
sampleNames |
character vector, names of samples/columns to be extracted. Set to NULL when summary data is for genes. |
geneNames |
character vector, names of genes to be extracted. Set to NULL when summary data is for samples |
A data frame with subset of input data and with the same orders as geneNames and sampleNames.
Henry Zhang
data(RNASeqDemoData) exprValue <- as.matrix(RNASeqDemoData[, 2:ncol(RNASeqDemoData)]) summaryData <- data.frame(as.character(RNASeqDemoData[,1]), rowMeans(exprValue), log2(rowMeans(exprValue))) geneSymbols <- c("ECM1", "SLC26A6", "ADAMTS13", "FCN3", "CFP") sumByGene <- getPlotSummaryData(summaryData, geneNames=geneSymbols) summaryData <- rbind(colMeans(exprValue), log2(colMeans(exprValue))) summaryData <- data.frame(c("sampleMean", "log2mean"), summaryData) colnames(summaryData) <- colnames(exprValue) sampleID <- colnames(exprValue)[c(2:21, 32:41)] sumBySample <- getPlotSummaryData(summaryData, sampleID)