Description Usage Arguments Value Author(s) See Also Examples
Run a competitive test to highlight whether a gene set is highly ranked in a sequence of gene values on the genes outside the gene-set.
1 | mwwGST(rankedList, geneSet, minLenGeneSet = 5, alternative = "greater", moreDetails = FALSE, verbose = TRUE)
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rankedList |
numeric vector of data values where the names are the genes names |
geneSet |
a character list of genes |
minLenGeneSet |
minimum dimension of the geneSet |
alternative |
a character string specifying the alternative hypothesis ("two.sided", "less", "greater"). |
moreDetails |
a logical indicating whether the output includes the rankedList (necessary to plot the enrichment) |
verbose |
a logical indicating to suppress or not the messages; it's TRUE by default. |
call |
a character string of the call of the function. |
alternative |
a character string describing the alternative hypothesis. |
originalGeneSetCount |
the length of the gene-set given in input |
actualGeneSet |
the list of genes as comes from the intesection between the gene-set and the ranked-list. |
actualGeneSetCount |
the length of the actualGeneSet |
rankedList |
the ranked-list given in input; this slot is filled whether moreDetails is TRUE |
lengthOfRankedList |
the length of the ranked-list given in input |
statistic |
the value of the Mann-Whitney-Wilcox test statistic. |
nes |
the value of the normalized enrichment score. |
pu |
is the probability unbalance, i.e. the ratio of nes to 1-nes. |
log.pu |
the log2 transformation of the pu. |
p.value |
the p-value for the test. |
Stefano M. Pagnotta
1 2 3 4 5 6 7 8 9 10 11 12 | library(yaGST)
data("rankedList")
# generate a random data set of dimension 100
geneSet <- sample(head(names(rankedList), 5000), 100)
ans <- mwwGST(rankedList, geneSet, moreDetails = TRUE)
ans
plot(ans)
# generate a second gene set
geneSet <- sample(tail(names(rankedList), 5000), 100)
ans <- mwwGST(rankedList, geneSet, moreDetails = TRUE)
plot(ans)
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