gseKEGG2 {signatureSearch} | R Documentation |
This modified Gene Set Enrichment Analysis (GSEA) of KEGG pathways supports gene test sets with large numbers of zeros.
gseKEGG2( geneList, organism = "hsa", keyType = "kegg", exponent = 1, nproc = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE, readable = FALSE )
geneList |
named numeric vector with gene ids in the name slot decreasingly ranked by scores in the data slot. |
organism |
supported organism listed in URL: http://www.genome.jp/kegg/catalog/org_list.html |
keyType |
one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
exponent |
weight of each step |
nproc |
if not equal to zero, sets |
nPerm |
permutation numbers |
minGSSize |
integer, minimum size of each gene set in annotation system |
maxGSSize |
integer, maximum size of each gene set in annotation system |
pvalueCutoff |
pvalue cutoff |
pAdjustMethod |
pvalue adjustment method |
verbose |
print message or not |
readable |
TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table. |
feaResult object
# Gene Entrez id should be used for KEGG enrichment data(geneList, package="DOSE") #geneList[100:length(geneList)]=0 #gsekk <- gseKEGG2(geneList=geneList, pvalueCutoff = 1) #head(gsekk)