getImat: Generate an indicator matrix

Description Usage Arguments Value Author(s) See Also Examples

Description

This function is used to generate an indicator matrix as an input to the pcot2 function. The gene category indicator matrix indicates presence or absence of genes in pre-defined gene sets (e.g., gene pathways). The indicator matrix contains rows representing gene identifiers of genes present in the expression data and columns representing pre-defined group names. A value of 1 indicates the presence of a gene and 0 indicates the absence for the gene in a particular group.

Usage

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getImat(x, pathlist, ms = 10)

Arguments

x

A matrix with no missing values; Each row represents a gene and each column represents a sample.

pathlist

A list of gene sets.

ms

The minimum gene set size. Gene sets containing less than this number of genes will be excluded from the analysis.

Value

An indicator matrix is returned. The matrix value is 1 (gene in) or 0 (gene out)

Author(s)

Sarah Song and Mik Black

See Also

pcot2,corplot,corplot2,aveProbe

Examples

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library(multtest)
library(hu6800.db)  
data(golub)
rownames(golub) <- golub.gnames[,3]
colnames(golub) <- golub.cl
KEGG.list <- as.list(hu6800PATH)
imat <- getImat(golub, KEGG.list, ms=10) 


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