subsetSamples

Create a SQM object containing only samples specified by the user, and the ORFs, contigs, bins, taxa and functions present in those samples.

'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.

Fernando Puente-Sánchez

SQMtools

Analyze Results Generated by the 'SqueezeMeta' Pipeline

Natalia García-García

subsetSamples function

<dl><dt>SQM</dt>
<dd>SQM object to be subsetted.</dd>
<dt>samples</dt>
<dd>character. Samples to be included in the subset.</dd>
<dt>remove_missing</dt>
<dd>bool. If <code>TRUE</code>, ORFs, contigs, bins, taxa and functions absent from the selected samples will be removed from the subsetted object (default <code>TRUE</code>).</dd></dl>

Arguments

Filter results by sample — subsetSamples

<dl>

<dt>SQM</dt>
<dd>SQM object to be subsetted.</dd>


<dt>samples</dt>
<dd>character. Samples to be included in the subset.</dd>


<dt>remove_missing</dt>
<dd>bool. If <code>TRUE</code>, ORFs, contigs, bins, taxa and functions absent from the selected samples will be removed from the subsetted object (default <code>TRUE</code>).</dd>

</dl>

subsetSamples: Filter results by sample

Description

Usage

Value

Arguments

See Also