readGeneFamilies {ShotgunFunctionalizeR}R Documentation

Read a data file

Description

Reads a metagenomic data file from disk.

Usage

readGeneFamilies(file, type.family="detect", sep="\t")

Arguments

file name of the filename
type.family type of gene families
sep field separator between the columns

Details

readGeneFamilies read a text file with metagenomic data and creats a list for further analysis. The text file should be in ANSI format and organized as follows. The left most column should be names 'GeneFamily' and contain the identifiers for the type of gene familiy used. The following columns should contain the counts for each of the samples. The first row should contain the name of the samples.

readGeneFamilies can detect which type of gene families that are used (type.family='detect'). This is achieved matching identifiers against those supported by ShotgunFunctionalizeR (currently clusters of orthologous genes (COG) and Enzyme Commision numbers (EC). Gene families of COG type are assumed if no valid match can be made.

Example files are available at http://shotgun.zool.gu.se.

Value

readGeneFamilies returns a list with the following elements

Data a matrix containing the counts for each gene familiy (rows) and each sample (columns)
Annotation descriptions for the gene families
Type string which indicate the type of gene familiy used

See Also

writeRankings

Examples

## Not run: data<-readGeneFamilies("MetagenomicData.txt")

[Package ShotgunFunctionalizeR version 1.0-2 Index]