normalizer: Normalizing Function

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Normalizing Function

Description

Actual function that normalizes data, one method at a time. In other words, it is called three times by runNormalization() if the data is to be scaled by samples, scaled by features, and transformed.

Usage

normalizer(
  data,
  norm_type,
  sum_scale = NA,
  log_base = NA,
  impute_method = c("GBM", "SQ", "BL", "CZM")
)

Arguments

data	Abundance table that will be normalized by in columns. In other words, if scaling by samples, then samples should be in columns. Does not matter for data transformation.
norm_type	Normalization type: "sum", "none", "relative", "standardized", "centered", "median", "range", "glog" (generalized log), "pseudolog", "log",
sum_scale	Number to scale samples/features to.
log_base	Base for log transformations.
impute_method	Method to impute zeros by if using zCompositions approach

Value

Normalized abundance table.

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