gc_position

Internal helper used by <code>gc_cal</code>.
Given the ordered positions of all reference genes on a contig
(<code>Data</code>) and the vector of cluster breakpoints produced by
<code>gc_cluster</code> (<code>Cluster</code>), this function slices
<code>Data</code> to return the positions that belong to the
<code>EachCluster</code>-th cluster.

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

gc_position function

<dl><dt>Data</dt>
<dd>A numeric vector (ascending order) of ORF positions that carry
one of the reference genes of interest. Usually the vector
<code>orf_position.tmp</code> created inside <code>gc_cal</code>.</dd>
<dt>Cluster</dt>
<dd>Numeric vector returned by <code>gc_cluster</code>; each
element marks the last position of a candidate cluster.</dd>
<dt>EachCluster</dt>
<dd>Integer index specifying which cluster to extract
(1 = first cluster, 2 = second cluster, …).</dd></dl>

Arguments

Extract ORF Positions for One Specific Gene Cluster — gc_position

<dl>

<dt>Data</dt>
<dd>A numeric vector (ascending order) of ORF positions that carry
one of the reference genes of interest. Usually the vector
<code>orf_position.tmp</code> created inside <code>gc_cal</code>.</dd>


<dt>Cluster</dt>
<dd>Numeric vector returned by <code>gc_cluster</code>; each
element marks the last position of a candidate cluster.</dd>


<dt>EachCluster</dt>
<dd>Integer index specifying which cluster to extract
(1 = first cluster, 2 = second cluster, …).</dd>

</dl>

gc_position: Extract ORF Positions for One Specific Gene Cluster

Description

Usage

Value

Arguments