length_filter

Filters BLAST hits by removing ORFs whose gene (protein) length
is an outlier within the corresponding gene group, as defined
by the inter-quartile range (IQR). Hits whose length falls
outside the interval
<code>[Q1 - down_IQR * IQR, Q3 + up_IQR * IQR]</code> are discarded.

Performs end-to-end analysis of gene clusters—such as photosynthesis,
carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral marker genes
(e.g., capsid, polymerase, integrase)—from genomes and metagenomes.
It parses Basic Local Alignment Search Tool (BLAST) results in tab-delimited
format produced by tools like NCBI BLAST+ and Diamond BLASTp, filters
Open Reading Frames (ORFs) by length, detects contiguous clusters of reference genes,
optionally extracts genomic coordinates, merges functional annotations, and
generates publication-ready arrow plots. The package works seamlessly with
or without the coding sequences input and skips plotting when no functional
groups are found. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

Liuyang Li

gclink

Gene-Cluster Discovery, Annotation and Visualization

length_filter function

<dl><dt>Data</dt>
<dd>A data frame containing BLAST results. Must include the columns
<code>gene</code> (gene symbol) and <code>length</code> (ORF length in amino
acids).</dd>
<dt>down_IQR</dt>
<dd>Numeric multiplier applied to the IQR for the lower
bound (default: 1.5).</dd>
<dt>up_IQR</dt>
<dd>Numeric multiplier applied to the IQR for the upper bound
(default: 1.5).</dd></dl>

Arguments

Remove Length Outliers from BLAST Results — length_filter

<dl>

<dt>Data</dt>
<dd>A data frame containing BLAST results. Must include the columns
<code>gene</code> (gene symbol) and <code>length</code> (ORF length in amino
acids).</dd>


<dt>down_IQR</dt>
<dd>Numeric multiplier applied to the IQR for the lower
bound (default: 1.5).</dd>


<dt>up_IQR</dt>
<dd>Numeric multiplier applied to the IQR for the upper bound
(default: 1.5).</dd>

</dl>

length_filter: Remove Length Outliers from BLAST Results

Description

Usage

Value

Arguments

Details