select.samples: Select samples based on metadata

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

Description

This functions selects labels and metadata based on a specific column in the metadata. Provided with a column-name in the metadata and a range or a set of allowed values, the function will filter the siamcat-class object accordingly.

Usage

select.samples(siamcat, filter, allowed.set = NULL, 
allowed.range = NULL, verbose = 1)

Arguments

siamcat	an object of class siamcat-class
filter	string, name of the meta variable on which the selection should be done
allowed.set	a vector of allowed values
allowed.range	a range of allowed values
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

Value

an object of class siamcat-class with labels and metadata filtered in order to contain only allowed values

Examples

    data(siamcat_example)
    # Select all samples that fall into an Age-range between 20 and 80 years
    siamcat_selected <- select.samples(siamcat_example, 'age',
    allowed.range=c(20, 80))

    # Select all samples for which information about the gender is given
    # Provide additional information with verbose
    ## Not run: siamcat_selected <- select.samples(siamcat_example, 'gender',
    allowed.set=c(1, 2), verbose=2)
## End(Not run)
    

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