select.samples: Select samples based on metadata

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

Description

This function select samples based on information given in the metadata

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	integer, 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 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.

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 25 and 80 years
siamcat_selected <- select.samples(siamcat_example,
    filter='Age',
    allowed.range=c(25, 80))

# Select only female samples
siamcat_female <- select.samples(siamcat_example,
    filter='Gender',
    allowed.set=c('F'))

SIAMCAT documentation built on Nov. 8, 2020, 5:14 p.m.