dcda: Domain Content Dissimilarity Analysis

Description Usage Arguments Value

View source: R/dcda.R

Description

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

Usage

1
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 Nov. 19, 2017, 2:24 p.m.