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

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_study-pop-I_N141_tax_profile_mocat_bn_specI_clusters.tsv', package = 'SIAMCAT') labels <- read.labels(fn.label)