filteringPaths

This function eliminates gene sets with low expression in both groups in
a study

Performing the different steps of gene set enrichment meta-analysis. It provides different functions that allow the application of meta-analysis based on the combination of effect sizes from different pathways in different studies to obtain significant pathways that are common to all of them.

Juan Antonio Villatoro-García

GSEMA

Gene Set Enrichment Meta-Analysis

Pablo Jurado-Bascón

Pedro Carmona-Sáez

filteringPaths function

<dl><dt>objectMApath</dt>
<dd>A list of list. Each list contains two elements.
The first element is the Gene Set matrix (gene sets in rows and samples in
columns) and the second element is a vector of zeros and ones that represents
the state of the different samples of the Gene Sets matrix.
0 represents one group (controls) and 1 represents the other group (cases).</dd>
<dt>threshold</dt>
<dd>A number that indicates the threshold to eliminate a gene
set. For a eliminate a gene set is necessary that the median for both groups
are less than the threshold
If threshold = "sd" the threshold will be the standard deviation of the
gene set. The default value is 0.65.</dd>
<dt>n_cores</dt>
<dd>A number that indicates the number of cores to use in the
parallelization. The default value is 1.</dd></dl>

Arguments

Juan Antonio Villatoro Garcia,
<a href="/link/juanantoniovillatorogarcia%40gmail.com?package=GSEMA&version=0.99.4" data-mini-rdoc="GSEMA::juanantoniovillatorogarcia@gmail.com">juanantoniovillatorogarcia@gmail.com</a>

Author

Fuction for filtering gene sets with low expression — filteringPaths

<dl>

<dt>objectMApath</dt>
<dd>A list of list. Each list contains two elements.
The first element is the Gene Set matrix (gene sets in rows and samples in
columns) and the second element is a vector of zeros and ones that represents
the state of the different samples of the Gene Sets matrix.
0 represents one group (controls) and 1 represents the other group (cases).</dd>


<dt>threshold</dt>
<dd>A number that indicates the threshold to eliminate a gene
set. For a eliminate a gene set is necessary that the median for both groups
are less than the threshold
If threshold = "sd" the threshold will be the standard deviation of the
gene set. The default value is 0.65.</dd>


<dt>n_cores</dt>
<dd>A number that indicates the number of cores to use in the
parallelization. The default value is 1.</dd>

</dl>

Juan Antonio Villatoro Garcia,
<a href='mailto:juanantoniovillatorogarcia@gmail.com'>juanantoniovillatorogarcia@gmail.com</a>

filteringPaths: Fuction for filtering gene sets with low expression

Description

Usage

Value

Arguments

Author

See Also

Examples