filter.features: Perform unsupervised feature filtering.

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

Description

This function performs unsupervised feature filtering. Features can be filtered based on abundance or prevalence. Additionally, unmapped reads may be removed.

Usage

filter.features(siamcat, filter.method = "abundance",
    cutoff = 0.001, recomp.prop = FALSE, rm.unmapped = TRUE, verbose = 1)

Arguments

siamcat	an object of class siamcat-class
filter.method	method used for filtering the features, can be one of these: c('abundance', 'cum.abundance', 'prevalence'), defaults to 'abundance'
cutoff	float, abundace or prevalence cutoff, default to 0.001
recomp.prop	boolean, should relative abundances be recomputed?, defaults to FALSE
rm.unmapped	boolean, should unmapped reads be discarded?, defaults to TRUE
verbose	control output: 0 for no output at all, 1 for only information about progress and success, 2 for normal level of information and 3 for full debug information, defaults to 1

Details

This function filters the features in a siamcat-class object in a unsupervised manner.

The different filter methods work in the following way:

• 'abundace' remove features whose abundance is never above the threshold value in any of the samples

• 'cum.abundance' remove features with very low abundance in all samples i.e. ones that are never among the most abundant entities that collectively make up (1-cutoff) of the reads in any sample

• 'prevalence' remove features with low prevalence across samples i.e. ones that are 0 (undetected) in more than (1-cutoff) proportion of samples.

Value

siamcat an object of class siamcat-class

Examples

    # Example dataset
    data(siamcat_example)
    # since the whole pipeline has been run in the example data, the feature
    # were filtered already.
    siamcat_example <- reset.features(siamcat_example)

# Simple examples
siamcat_filtered <- filter.features(siamcat_example,
    filter.method='abundance',
    cutoff=1e-03)

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