Description Usage Arguments Value Author(s) See Also Examples
Different enrichment analysis methods usually result in different gene set rankings for the same dataset. This function allows to combine results from the different set-based and network-based enrichment analysis methods. This includes the computation of average gene set ranks across methods.
1 2 3 4 5 6 7 | combResults(
res.list,
rank.col = configEBrowser("PVAL.COL"),
decreasing = FALSE,
rank.fun = c("comp.ranks", "rel.ranks", "abs.ranks"),
comb.fun = c("mean", "median", "min", "max", "sum")
)
|
res.list |
A list of enrichment analysis result lists (as returned by
the functions |
rank.col |
Rank column. Column name of the enrichment analysis result table that should be used to rank the gene sets. Defaults to the gene set p-value column, i.e. gene sets are ranked according to gene set significance. |
decreasing |
Logical. Should smaller (decreasing=FALSE, default) or larger (decreasing=TRUE) values in rank.col be ranked better? In case of gene set p-values the smaller the better, in case of gene set scores the larger the better. |
rank.fun |
Ranking function. Used to rank gene sets according to the
result table of individual enrichment methods (as returned from the
|
comb.fun |
Rank combination function. Used to combine gene set ranks across methods. Can be either one of the predefined functions (mean, median, max, min, sum) or a user-defined function. Defaults to 'sum', i.e. the rank sum across methods is computed. |
An enrichment analysis result list that can be detailedly explored
by calling eaBrowse
and from which a flat gene set ranking
can be extracted by calling gsRanking
.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | # (1) expression data:
# simulated expression values of 100 genes
# in two sample groups of 6 samples each
se <- makeExampleData(what="SE")
se <- deAna(se)
# (2) gene sets:
# draw 10 gene sets with 15-25 genes
gs <- makeExampleData(what="gs", gnames=names(se))
# (3) make artificial enrichment analysis results:
# 2 ea methods with 5 significantly enriched gene sets each
ora.res <- makeExampleData(what="ea.res", method="ora", se=se, gs=gs)
gsea.res <- makeExampleData(what="ea.res", method="gsea", se=se, gs=gs)
# (4) combining the results
res.list <- list(ora.res, gsea.res)
comb.res <- combResults(res.list)
# (5) result visualization and exploration
gsRanking(comb.res)
# user-defined ranking and combination functions
# (a) dummy ranking, give 1:nrow(res.tbl)
dummy.rank <- function(res.tbl) seq_len(nrow(res.tbl))
# (b) weighted average for combining ranks
wavg <- function(r) mean(c(1,2) * r)
comb.res <- combResults(res.list, rank.fun=dummy.rank, comb.fun=wavg)
|
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