ReadData: Read in CSV file

In Mathelab/IntLIM: Integration of Omics Data Using Linear Modeling

Read in CSV file

Description

The metadata associated with data files to be analyzed in IntLim is supplied as a CSV file with two columns and 6 rows: type,filenames metabData,myfilename geneData,myfilename metabMetaData,myfilename (optional) geneMetaData,myfilename (optional) sampleMetaData,myfilename

Usage

ReadData(inputFile, metabid = NULL, geneid = NULL, logmetab = FALSE,
  loggene = FALSE)

Arguments

inputFile	input file in CSV format (see Despcription)
metabid	name of column from metabolite meta data to be used as id (required if a metabolite meta dadta file is present, must match metabolite abundances data)
geneid	name of column from gene meta data to be used as id (required if a gene meta data file is present, must match gene expression data)
logmetab	whether or not to log metabolite values (T/F)
loggene	whether or not to log gene values (T/F)

Details

Note that all files supplied in the CSV file, and the CSV file itself should be placed in the same folder. The software assumes will automatically retrieve the file path of the input files (based on location of CSV files). Note also that the input data files should be in a specific format: metabData: rows are metabolites, columns are samples geneData: rows are genes, columns are samples metabMetaData: rows are metabolites, features are columns geneMetaData: rows are genes, features are columns sampleMetaData: rows are samples, features are columns In addition, the first column of the sampleMetaData file is assumed to be the sample id, and those sample ids should match the columns of metabData and geneData (e.g. it is required that all sample ids in the metabData and geneData are also in the sampleMetaDatafile).

Value

MultiDataSet object with input data

Examples

dir <- system.file("extdata", package="IntLIM", mustWork=TRUE)
csvfile <- file.path(dir, "NCItestinput.csv")
mydata <- ReadData(csvfile,metabid='id',geneid='id')

Mathelab/IntLIM documentation built on July 9, 2022, 5:10 p.m.