getPlotSummaryData: Extract Summary Subset for Plotting

In caOmicsV: Visualization of multi-dimentional cancer genomics data

Description

Extract required rows and columns from a summary data set.

Usage

    getPlotSummaryData(summaryData, sampleNames=NULL, geneNames=NULL)

Arguments

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

Value

A data frame with subset of input data and with the same orders as geneNames and sampleNames.

Author(s)

Henry Zhang

Examples

    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)

caOmicsV documentation built on Nov. 8, 2020, 8:23 p.m.