Rarefaction step within read_input_data — rarefied_microbiome • RITHMS

Rarefaction step within read_input_data

Usage

rarefied_microbiome(microbiome_matrix, id_column = "ind_id", threshold = 0.05)

Arguments

microbiome_matrix: Microbiome counting table, OTUs in columns and a column specifying the IDs
id_column: String specifying the name of the column containing the individual IDs. Default is "ind_id"
threshold: Minimum prevalence threshold

Value

The filtered microbiome matrix, without OTUs whose prevalence is lower than the set threshold

See also

read_input_data(), generate_founder()

Examples

if (FALSE) { # \dontrun{
  microbiome <- data.table::fread("/path/to/microbiome.txt")
  microbiome_filtered <- rarefied_microbiome(microbiome, id_columns = "sample_id", threshold = 0.05)
} # }