select.samples {SIAMCAT}R Documentation

Select samples based on metadata

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('F'), verbose=2)
## End(Not run)
[Package SIAMCAT version 1.2.1 Index]