Learn R Programming

manta (version 1.18.0)

outGenes: find the most significant or highest fold change outlier genes

Description

.

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

Run this code


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

de <- exactTest(x)
outGenes(de)

Run the code above in your browser using DataLab