orthologyMatrix: Construct orthology matrices

In gschofl/genoslideR: Create and manipulate multiple genome alignments with annotation.

Description

Constructs pairwise orthology matrices for all combinations of species as provided by the base_names argument based on reciprocal best BLAT hits. Use mergeOrthologyMatrix to merge these pairwise comparison into a single data frame.

Usage

orthologyMatrix(blat_dir, base_names = NULL, pident_threshold = 60,
  paln_threshold = 40, name_sep = "-", log = TRUE)

Arguments

blat_dir	Directory where the anchor and hit files produced by link{mercator} live.
base_names	Species for which an orthology matrix should be constructed. Must correspond to the relevant filenames minus extension. If NULL all are selected
pident_threshold	Threshold for (cumulative) percentage of sequence identity
paln_threshold	Threshhold for (cumulative) percentage of alignment length (query coverage).
name_sep	String that separates two compared species in filenames.
log	Write logfiles

Value

A list of class ‘orthoMatrix’, which is essentially a list of dgCMatrixes with attributes ‘labels’, ‘nGenes’, and ‘combinations’ attached.

gschofl/genoslideR documentation built on May 17, 2019, 8:52 a.m.