transData: Data Transformation

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Data Transformation

Description

Data Transformation

Usage

transData(
  dataset = NULL,
  temp = F,
  trans_method = c("clr", "glog", "pseudolog", "log", "gmpr", "none"),
  log_base = 10,
  impute_method = c("GBM", "SQ", "BL", "CZM"),
  silent = F
)

Arguments

dataset	MicroVis dataset (mvdata object)
temp	If set to TRUE, it tells processDataset() to NOT update the active dataset.
trans_method	Method for transforming data. Choices are "glog" (generalized log), "none", "pseudolog", and "log".
log_base	Base of log transformation.
impute_method	Method to impute zeros by if using zCompositions approach
silent	Argument that is ultimately passed onto runSampleFilter(), runNormalization(), and runFeatureFilter(), telling them not to output any messages.

Value

Microvis dataset (mvdata object) with samples scaled.

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