read.features: Read feature file

In KonradZych/SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes

Description

This file reads in the tsv file with features and converts it into a matrix.

The file should be oragnized as follows: features (in rows) x samples (in columns).

First row should contain sample labels (consistent with label data), while the first column should contain feature labels (e.g. taxonomic identifiers). The remaining entries are expected to be real values >= 0 that quantify the abundance of each feature in each sample.

Usage

read.features(fn.in.feat, transpose = FALSE, verbose = 0)

Arguments

fn.in.feat	name of the tsv file containing features
transpose	should the features table be transposed?
verbose	control output: 0 for no output at all, 1 for information about progress and time, defaults to 0

Value

otu_table containing features from the file

Examples

    # run with example data
    fn.feat <- system.file('extdata', 'feat_crc_zeller_msb_mocat_specI.tsv',
    package = 'SIAMCAT')

    features <- read.features(fn.feat)

KonradZych/SIAMCAT documentation built on May 17, 2019, 6:20 p.m.