outGenes {manta} | R Documentation |
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outGenes(x, n=50, p=.05, FC=1, A.pct=.05, uk.filter=NULL, method='BH', verbose=TRUE)
x |
a MANTA object. |
n |
number of genes to return. |
p |
adjusted p-value cut-off. |
FC |
fold change cut-off. |
A.pct |
percentage of genes that should be right most outliers. |
uk.filter |
a character vector of unknown gene name paterns to filter out (eg 'lcl'). |
method |
multiple testing correction method from p.adjust |
verbose |
should the function print these results (or just return the table) |
a table of the outlier genes
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manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta") load(manta.path) de <- exactTest(x) outGenes(de)