read.meta: Read metadata file

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

Description

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

The file should be organized as follows: samples (in rows) x metadata (in columns). Metadata needs to be converted to numerical values by the user.

Metadata may be optional for the SIAMCAT workflow, but are necessary for heatmap displays, see model.interpretation.plot

Usage

read.meta(fn.in.meta)

Arguments

fn.in.meta

name of the tsv file containing metadata

Value

sample_data object

Examples

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

meta_data <- read.meta(fn.meta)

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