domAbundance: Domain Abundance for each sample

Description Usage Arguments Value

Description

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

Usage

1
domAbundance(fastas, pfamA, cut = "ga", 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.

cpus

integer The number of cpus to use.

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.

Value

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


iferres/misp_test documentation built on May 5, 2019, 12:32 p.m.