MicrobIEM_decontamination: Microbiem decontamination by Luise Rauer, TUM Munich

In peterolah001/BiMiCo: Biomap Microbiome Core methods

Microbiem decontamination by Luise Rauer, TUM Munich

Description

Numeric thresholds for filtering contaminants, default is to not use any filter (NA) ratio_NEG1_threshold = NA, # Sensible thresholds: > 0 ratio_NEG2_threshold = NA, # Sensible thresholds: > 0 span_NEG1_threshold = NA, # Sensible thresholds: between 0 and 1 span_NEG2_threshold = NA # Sensible thresholds: between 0 and 1

Usage

MicrobIEM_decontamination(feature_table, SAMPLE, NEG1 = character(0),
  NEG2 = character(0), ratio_NEG1_threshold = NA,
  ratio_NEG2_threshold = NA, span_NEG1_threshold = NA,
  span_NEG2_threshold = NA)

Arguments

feature_table	(Required) data.frame, a feature table with count data, with ASVs/OTUs/taxa in rows, ASV IDs as rownames, and samples in columns
SAMPLE	(Required) character vector, names of samples to be filtered
NEG1	(Optional) character vector, names of NEG1 controls, can by empty
NEG2	(Optional) character vector of names of NEG2 controls, can be empty
ratio_NEG1_threshold	(Optional) Numeric, thresholds for filtering contaminants, default is to not use any filter (NA)
ratio_NEG2_threshold	(Optional) Numeric, thresholds for filtering contaminants, default is to not use any filter (NA)
span_NEG1_threshold	(Optional) Numeric, thresholds for filtering contaminants, default is to not use any filter (NA)
span_NEG2_threshold	(Optional) Numeric, thresholds for filtering contaminants, default is to not use any filter (NA)

Examples

MicrobIEM_decontamination()

peterolah001/BiMiCo documentation built on April 24, 2023, 3:35 a.m.