getPlotSummaryData {caOmicsV} | R Documentation

## Extract Summary Subset for Plotting

### 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)

[Package caOmicsV version 1.10.0 Index]