ApplyContrasts

Helper function to run many pairwise comparisons using a contrast matrix

Nucleotide conversion sequencing experiments have been
developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such
experiments require specialized tools for primary processing such as GRAND-SLAM,
(see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for
downstream analyses. 'grandR' provides a comprehensive toolbox for quality control,
kinetic modeling, differential gene expression analysis and visualization of such data.

Florian Erhard

grandR

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Teresa Rummel

Lygeri Sakellaridi

Kevin Berg

ApplyContrasts function

<dl><dt>data</dt>
<dd>the grandR object</dd>
<dt>analysis</dt>
<dd>a plain name, only used for status messages</dd>
<dt>name.prefix</dt>
<dd>the prefix for the new analysis name; a dot and the column names of the contrast matrix are appended; can be NULL (then only the contrast matrix names are used)</dd>
<dt>contrasts</dt>
<dd>contrast matrix that defines all pairwise comparisons, generated using GetContrasts</dd>
<dt>mode.slot</dt>
<dd>which slot to take expression values from</dd>
<dt>genes</dt>
<dd>restrict analysis to these genes; NULL means all genes</dd>
<dt>verbose</dt>
<dd>print status messages?</dd>
<dt>FUN</dt>
<dd>a function taking 1. the data matrix, 2. a logical vector indicating condition A and 3. a logical vector indicating condition B</dd>
<dt>...</dt>
<dd>further parameters forward to FUN</dd></dl>

Arguments

Apply a function over contrasts — ApplyContrasts

<dl>

<dt>data</dt>
<dd>the grandR object</dd>


<dt>analysis</dt>
<dd>a plain name, only used for status messages</dd>


<dt>name.prefix</dt>
<dd>the prefix for the new analysis name; a dot and the column names of the contrast matrix are appended; can be NULL (then only the contrast matrix names are used)</dd>


<dt>contrasts</dt>
<dd>contrast matrix that defines all pairwise comparisons, generated using GetContrasts</dd>


<dt>mode.slot</dt>
<dd>which slot to take expression values from</dd>


<dt>genes</dt>
<dd>restrict analysis to these genes; NULL means all genes</dd>


<dt>verbose</dt>
<dd>print status messages?</dd>


<dt>FUN</dt>
<dd>a function taking 1. the data matrix, 2. a logical vector indicating condition A and 3. a logical vector indicating condition B</dd>


<dt>...</dt>
<dd>further parameters forward to FUN</dd>

</dl>

ApplyContrasts: Apply a function over contrasts

Description

Usage

Value

Arguments

Details

See Also