filter_dm: Filter samples from dissimilarity matrix

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Filter samples from dissimilarity matrix

Description

Filter out or keep particular samples in a dissimilarity matrix based on contextual metadata.

Usage

filter_dm(input_dm, filter_cat, filter_vals, keep_vals)

Arguments

input_dm	The input dissimilarity matrix with corresponding mapping file as generated by load_dm or calc_mean_dissimilarities with the option to produce a resulting metadata map.
filter_cat	The metadata map header string for the factor you would like to use to filter samples.
filter_vals	The values within the filter category (vector or single value) you would like to use to remove samples from the dissimilarity matrix and metadata map.
keep_vals	Alternatively, keep only samples represented by these values.

Value

A list variable with (1) the loaded dissimilarity matrix and (2) the loaded mapping file.

Examples

# rarefy
fruits_veggies_rar = single_rarefy(fruits_veggies, 1000)
# calculate dissimilarities
dm = calc_dm(fruits_veggies_rar$data_loaded)
# calculated mean dissimilarities by sample type
dm_means = calc_mean_dissimilarities(dm = dm,
                                     metadata_map = fruits_veggies$map_loaded,
                                     summarize_by_factor = 'Sample_type',
                                     return_map = TRUE)
# filter sample types to include only lettuce and spinach
filter_dm(input_dm = dm_means, filter_cat = 'Sample_type',
          keep_vals = c('Lettuce', 'Spinach'))

leffj/mctoolsr documentation built on Aug. 5, 2022, 1:27 a.m.