normalizeTable: Normalize a Standalone Abundance Table

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Normalize a Standalone Abundance Table

Description

Normalize a Standalone Abundance Table

Usage

normalizeTable(
  abundance_table,
  sample_scale = NULL,
  feature_scale = NULL,
  transformation = NULL,
  sum_scale = 1e+06,
  log_base = 10,
  silent = F
)

Arguments

abundance_table	Abundance table with samples as rows and features as columns
sample_scale	Sample scaling method to be used. Choices are "sum", "none", "relative", "median", "range", "centered", and "standardized". Default is "sum".
feature_scale	Feature scaling method to be used. Choices are "sum", "none", "relative", "median", "range", "centered", and "standardized". Default is "sum".
transformation	Transformation method to be used. Choices are "glog" (generalized log), "none", "pseudolog", and "log".
sum_scale	Number to scale samples/features by. Default is 1 million.
log_base	Base for log transformations. Default is 10
silent	Argument that is ultimately passed onto runSampleFilter(), runNormalization(), and runFeatureFilter(), telling them not to output any messages.

Value

Normalized abundance table.

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.