read.label: Read label file

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

Description

Read label information from a file

Usage

read.label(fn.in.label)

Arguments

fn.in.label

name of the tsv file containing labels

Details

This function reads in a tsv file with labels and converts it into a label.

First row is expected to be

#BINARY:1=[label for cases]; -1=[label for controls].

Second row should contain the sample identifiers as tab-separated list (consistent with feature and metadata).

Third row is expected to contain the actual class labels (tab-separated): 1 for each case and -1 for each control.

Note: Labels can take other numeric values (but not characters or strings); importantly, the label for cases has to be greater than the one for controls

Value

label object containing several entries:

• $label named vector containing the numerical labels from the file;

• $info information about the classes in the label;

• $type information about the label type (e.g. BINARY);

Examples

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

crc.zeller.label <- read.label(fn.label)

SIAMCAT documentation built on Nov. 8, 2020, 5:14 p.m.