Description Author(s) See Also
This page gives an overview of the LIMMA functions for gene set testing and pathway analysis.
roast
Self-contained gene set testing for one set. Uses zscoreT
to normalize t-statistics.
mroast
Self-contained gene set testing for many sets. Uses zscoreT
to normalize t-statistics.
fry
Fast approximation to mroast
, especially useful when heteroscedasticity of genes can be ignored.
camera
Competitive gene set testing.
romer
and topRomer
Gene set enrichment analysis.
ids2indices
Convert gene sets consisting of vectors of gene identifiers into a list of indices suitable for use in the above functions.
alias2Symbol
, alias2SymbolTable
and alias2SymbolUsingNCBI
Convert gene symbols or aliases to current official symbols.
geneSetTest
or wilcoxGST
Simple gene set testing based on gene or probe permutation.
barcodeplot
Enrichment plot of a gene set.
goana
and topGO
Gene ontology over-representation analysis of gene lists using Entrez Gene IDs.
goana
can work directly on a fitted model object or on one or more lists of genes.
kegga
and topKEGG
KEGG pathway over-representation analysis of gene lists using Entrez Gene IDs.
kegga
can work directly on a fitted model object or on one or more lists of genes.
Gordon Smyth
01.Introduction, 02.Classes, 03.ReadingData, 04.Background, 05.Normalization, 06.LinearModels, 07.SingleChannel, 08.Tests, 09.Diagnostics, 10.GeneSetTests, 11.RNAseq
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