prepSupMoa {mogsa} | R Documentation |
Convert a list of gene set information to a set of sumpplementary tables that can be used as input of function "sup.moa" or "mogsa".
prepSupMoa(X, geneSets, minMatch = 10, maxMatch = 500)
X |
A matrix/data.frame or a list of matrix/data.frame or a list of character vector. If it is a list of matrix/data.frame, row names of matrix/data.frame will be used to create the projection matrix. Otherwise the charater vectors will used to create the supplementary matirx. |
geneSets |
Gene sets list or an object of class "GeneSet" or "GeneSetCollection". A gene set list could be returned by prepGraphite or prepMolsigDB. |
minMatch |
The minimum match of geneset. |
maxMatch |
The maximum match genesets. |
Details here
A list of matrix could used as supplementary tables by "sup.moa" or "mogsa".
Chen Meng
See Also as prepGraphite
and prepMsigDB
.
library(graphite) data(NCI60_4arrays) kegg <- pathways(species = "hsapiens", "kegg") pw <- c("Purine metabolism", "Endocrine resistance", "MAPK signaling pathway") gss <- prepGraphite(db = kegg[pw], id="symbol") gss <- lapply(gss, function(x) sub("SYMBOL:", "", x)) sup_data1 <- prepSupMoa(NCI60_4arrays, geneSets=gss) gene_list <- lapply(NCI60_4arrays, rownames) sup_data2 <- prepSupMoa(gene_list, geneSets=gss)