closestHomolog: Uses pairwise sequence similarity search results in order to...

In asishallab/GeneFamilies: Analyses different properties of gene families

Uses pairwise sequence similarity search results in order to identify which gene is the closest homolog of the argument gene.id. Self-Matches are excluded and as measure of sequence similarity the Bit-Score is used.

Description

Uses pairwise sequence similarity search results in order to identify which gene is the closest homolog of the argument gene.id. Self-Matches are excluded and as measure of sequence similarity the Bit-Score is used.

Usage

closestHomolog(gene.id, seq.sim.tbl = if (exists("all.vs.all.sim"))
  all.vs.all.sim, gene.col.a = "V1", gene.col.b = "V2",
  bit.score.col = "V12")

Arguments

gene.id	The accession of the gene for which to find it's closest homolog.
seq.sim.tbl	An instance of base::data.frame holding the tabular output of the pairwise sequence similarity searches. Could be generated by using BLAT or Blast. Default is if (exists('all.vs.all.sim')) all.vs.all.sim.
gene.col.a	The column-name of seq.sim.tbl in which to find argument gene.id. MUST be a string not a number. Default is 'V1'
gene.col.b	The column-name of seq.sim.tbl in which to find gene accessions ('hits') of significant similarity to the argument gene gene.id. MUST be a string not a number. Default is 'V2'
bit.score.col	The column name of seq.sim.tbl in which to find the numeric Bit-Scores of the pairwise local sequence alignments, generated by Blast or BLAT e.g. MUST be a name not a number. Default is 'V12'.

Value

The gene identifier (accession) of that gene that has the highest Bit-Score in the pairwise comparisons with the argument gene gene.id. If no such gene can be found NA is returned.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.