plotlrt {MAST} | R Documentation

## Plot a likelihood ratio test object

### Description

Constructs a forest-like plot of signed log10 p-values, possibly adjusted for multiple comparisons `adjust` can be one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

### Usage

    plotlrt(lr, adjust = "fdr", thres = 0.1, trunc = 1e-06,
      groups = NULL)

### Arguments

`lr` | output from lrtest, with returnall=FALSE
`adjust` | `character`, passed along to `p.adjust`, see below
`thres` | `numeric` genes with adjusted pvalues above this value are not depicted
`trunc` | `numeric` p values below this value are truncated at this value
`groups` | `character` grouping value. If provided, must match groups argument passed to lrtest. Plots done separately for each group.

### Value

Constructs a dotplot

### Author(s)

andrew

[Package MAST version 1.12.0 Index]