outGenes {manta} | R Documentation

## find the most significant or highest fold change outlier genes

### 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)

[Package manta version 1.26.0 Index]