select.samples: Select samples based on metadata

In zellerlab/siamcat: Statistical Inference of Associations between Microbial Communities And host phenoTypes

Select samples based on metadata

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'))

zellerlab/siamcat documentation built on Feb. 1, 2024, 2:21 a.m.