Read gene-level expression summaries

Description

The function reads pre-pocessed and summarized gene-level expression data from file, and builds a data.frame with the information. The data.frame will have the same structure as the input summary file, i.e., genes in rows and samples in columns.

Usage

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    readGeneSummaries(useToyData, summaryFile)

Arguments

useToyData

Boolean argument to indicate whether sample data sets included in the TIN package should be used in the analysis.

summaryFile

Tab separated file with expression values for each combination of gene (row) and sample (column). Gene expression summary files can be obtained by using for instance APT (Affymetrix Power Tools) or Expression Console. The file is expected to have one initial header line with sample names, and one initial column with Affymetrix transcript cluster id's as row names.

Value

A data.frame with gene summary values. It consists of one column for each sample, and one row for each gene.

Examples

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# Read pre-processed gene summary values from file
# To use sample test data included in the TIN package as input:
    gs <- readGeneSummaries(useToyData=TRUE)
# To use your own data, provide path to txt file with expression values:
#   gs <- readGeneSummaries("/tmp/path/to/GeneLevelExpressionValues.txt")