RecA: RecA/RadA recombinase

In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

RecA/RadA recombinase

Description

The recombination protein RecA/RadA is essential for the repair and maintenance of DNA, and has homologs in every bacteria and archaea. By dividing the coverage of functions by the coverage of RecA, abundances can be transformed into copy numbers, which can be used to compare functional profiles in samples with different sequencing depths. RecA-derived copy numbers are available in the SQM object (SQM$functions$<annotation_type>$copy_number).

Usage

data(RecA)

Format

Character vector with the COG identifier for RecA/RadA.

Source

EggNOG Database.

Examples

data(Hadza)
data(RecA)
### Let's calculate the average copy number of each function in our samples.
# We do it for COG annotations here, but we could also do it for KEGG or PFAMs.
COG.coverage = Hadza$functions$COG$cov
COG.copynumber = t(t(COG.coverage) / COG.coverage[RecA,]) # Sample-wise division by RecA coverage.

SQMtools documentation built on April 3, 2025, 6:16 p.m.