getImat {pcot2} | R Documentation |
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.
getImat(x, pathlist, ms = 10)
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. |
An indicator matrix is returned. The matrix value is 1 (gene in) or 0 (gene out)
Sarah Song and Mik Black
S.Song and M.Black (2006) PCOT2: an R package for assessing expression changes in groups of related genes. Submitted to Bioinformatics.
pcot2
,corplot
,corplot2
,aveProbe
library(multtest) library(hu6800) data(golub) rownames(golub) <- golub.gnames[,3] colnames(golub) <- golub.cl KEGG.list <- as.list(hu6800PATH) imat <- getImat(golub, KEGG.list, ms=10)