outliers: find the most significant or highest fold change outlier...

In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description

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Usage

outGenes(x, n=50, p=.05, FC=1, A.pct=.05, uk.filter=NULL, method='BH',  verbose=TRUE)

Arguments

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)

Value

a table of the outlier genes

See Also

topTags

Examples

manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
load(manta.path)

de <- exactTest(x)
outGenes(de)

armbrustlab/manta documentation built on Dec. 17, 2019, 12:06 a.m.