filter_experiment: filter_experiment(ExpObj = NULL, featmaxatleastPPM = 0,...

In johnmcculloch/JAMS_BW: Just A Microbiology System

filter_experiment(ExpObj = NULL, featmaxatleastPPM = 0, featcutoff = c(0, 0), discard_SDoverMean_below = NULL, samplesToKeep = NULL, featuresToKeep = NULL, normalization = "relabund", asPPM = TRUE, PPM_normalize_to_bases_sequenced = FALSE, flush_out_empty_samples = FALSE, GenomeCompletenessCutoff = NULL, PctFromCtgscutoff = NULL)

Description

Filters a SummarizedExperiment object by several criteria.

Usage

filter_experiment(
  ExpObj = NULL,
  featmaxatleastPPM = 0,
  featcutoff = c(0, 0),
  discard_SDoverMean_below = NULL,
  samplesToKeep = NULL,
  featuresToKeep = NULL,
  normalization = "relabund",
  asPPM = TRUE,
  PPM_normalize_to_bases_sequenced = FALSE,
  flush_out_empty_samples = FALSE,
  GenomeCompletenessCutoff = NULL,
  PctFromCtgscutoff = NULL
)

johnmcculloch/JAMS_BW documentation built on April 30, 2024, 8:09 p.m.