create_bin

Create a bin from a vector of contigs

'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

create_bin function

<dl><dt>SQM</dt>
<dd>A SQM object.</dd>
<dt>bin</dt>
<dd>character. Name of the bin to be created.</dd>
<dt>contigs</dt>
<dd>character. Vector with the names of the contigs that will be included in the new bin.</dd>
<dt>delete_overlapping_bins</dt>
<dd>logical. If <code>TRUE</code>, bins that originally contained any of the provided contigs will be removed from the object. Default <code>FALSE</code>.</dd></dl>

Arguments

Create a bin from a vector of contigs — create_bin

<dl>

<dt>SQM</dt>
<dd>A SQM object.</dd>


<dt>bin</dt>
<dd>character. Name of the bin to be created.</dd>


<dt>contigs</dt>
<dd>character. Vector with the names of the contigs that will be included in the new bin.</dd>


<dt>delete_overlapping_bins</dt>
<dd>logical. If <code>TRUE</code>, bins that originally contained any of the provided contigs will be removed from the object. Default <code>FALSE</code>.</dd>

</dl>

create_bin: Create a bin from a vector of contigs

Description

Usage

Value

Arguments

See Also