filter_samples_by_counts: Filter samples from a dataset based on number of sequences

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Filter samples from a dataset based on number of sequences

Description

This function is useful for removing samples that have a low number of sequences.

Usage

filter_samples_by_counts(input, min_seqs)

Arguments

input	The input dataset as loaded by load_taxa_table.
min_seqs	A sample must have at minimum this number of sequences in order to be retained.

Value

A list variable with (1) the loaded taxa table, (2) the loaded mapping file, and optionally (3) the loaded taxonomy information.

Examples

# see number of sequences per sample
sort(colSums(fruits_veggies$data_loaded))
# remove samples with less than 1100 sequences
filter_samples_by_counts(fruits_veggies, min_seqs = 1100)

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