dcda: Domain Content Dissimilarity Analysis

In iferres/dcda: Domain Content Dissimilarity Analysis

Description

Compute Pfam-A domain content dissimilarity between two or more proteomes.

Usage

dcda(fastas, pfamA, cut = "ga", distMethod = "bray", cpus = 1L)

Arguments

fastas	A character vector giving the file names of the amino acid fasta files.
pfamA	character The path to the Pfam-A.hmm file
cut	Parameter controlling model-specific thresholding. Can be ethier "ga" or "tc". See HMMER 3.1b2 manual for more information.
distMethod	Dissimilarity index, partial match to "manhattan", "euclidean", "canberra", "bray" (DEFAULT), "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis". See vegdist for more information.
cpus	integer The number of cpus to use.

Value

A list object. The first element is the abundance matrix and the second is the dist matrix.

iferres/dcda documentation built on May 31, 2019, 11:51 p.m.