read.labels: Read labels file

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

Description

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

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

Usage

read.labels(fn.in.label)

Arguments

fn.in.label

name of the tsv file containing labels

Value

label object containing several entries:

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

• $header first row of the label file;

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

• $positive.lab numerical label for controls, e.g. -1;

• $negative.lab numerical label for cases, e.g. 1;

• $n.idx logical vector of labels (TRUE for controls, FALSE otherwise);

• $n.lab label for controls, e.g. healthy;

• $p.idx logical vector of labels (TRUE for cases, FALSE otherwise);

• $p.lab label for cases, e.g. cancer

Examples

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

labels <- read.labels(fn.label)

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