plotMA

a <code>data.frame</code> with columns <code>baseMean</code>,
    and <code>log2FoldChange</code>. In addition, if the argument <code>col</code> is left at
    its default, this <code>data.frame</code> also needs to have a column named <code>padj</code>.

colour used for the horizontal line at y=0.

linecol

arguments that are passed on to <code>plot.default</code>.

ylim, col, xlab, ylab, log, cex, ...


A simple helper function that makes a so-called "MA-plot", i.e. a
scatter plot of logarithmic fold changes (on the y-axis) versus the mean of
normalized counts (on the x-axis).

Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution

Simon Anders

DESeq

Differential gene expression analysis based on the negative
binomial distribution

plotMA function

a <code>DESeqResults</code> object produced by <code><a href="results" rd-options="">results</a></code>;
or a <code>DESeqDataSet</code> processed by <code><a href="DESeq" rd-options="">DESeq</a></code>, or the
individual functions <code><a href="nbinomWaldTest" rd-options="">nbinomWaldTest</a></code> or <code><a href="nbinomLRT" rd-options="">nbinomLRT</a></code>

object

the significance level for thresholding adjusted p-values

alpha

main

optional defaults to "mean of normalized counts"

xlab

ylim

whether to plot the MLE (unshrunken estimates), defaults to FALSE.
Requires that <code><a href="results" rd-options="">results</a></code> was run with <code>addMLE=TRUE</code>.
Note that the MLE will be plotted regardless of this argument, if DESeq() was run
with <code>betaPrior=FALSE</code>.

further arguments passed to <code>plotMA</code> if object
is <code>DESeqResults</code> or to <code><a href="results" rd-options="">results</a></code> if object is
<code>DESeqDataSet</code>

A simple helper function that makes a so-called "MA-plot", i.e. a
scatter plot of log2 fold changes (on the y-axis) versus the mean of
normalized counts (on the x-axis).

plotMA: Makes a so-called "MA-plot"

Description

Usage

Arguments

Value

Details

Examples