summary.SQM

Computes different statistics of the data contained in the SQM object.

'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

summary.SQM function

<dl><dt>object</dt>
<dd>SQM object to be summarized.</dd>
<dt>...</dt>
<dd>Additional parameters (ignored).</dd></dl>

Arguments

summary method for class SQM — summary.SQM

<dl>

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


<dt>...</dt>
<dd>Additional parameters (ignored).</dd>

</dl>

summary.SQM: summary method for class SQM

Description

Usage

Value

Arguments