marker.normalization: Normalization for markers' expression

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Normalization for markers' expression

Description

It normalizes expression abnormalities within selected markers.

Usage

marker.normalization(
  fcs.SCE,
  assay.i = "transformed",
  method,
  marker,
  new.matrix.name = "normalized"
)

Arguments

fcs.SCE	A fcs.SCE object generated through FlowCT::fcs.SCE().
assay.i	Name of matrix stored in the fcs.SCE object from which calculate correlation. Default = "transformed".
method	Methodology to perform each marker normalization. Possible values are "gauss" or "warp" (from flowStats package).
marker	Marker name(s) to normalize (based on visual inspection with FlowCT::multidensity()).
new.matrix.name	New normalized matrix name (it will stored within the fcs.SCE object). Default = "normalized".

Examples

## Not run: 
 fcs_gauss <- normalization.flw(fcs.SCE = fcs, method = "gauss", 
     marker = c("CD62L", "CCR4", "SSC_A"))
 fcs_warp <- normalization.flw(fcs.SCE = fcs, method = "warp", 
     marker = c("CD62L", "CCR4", "SSC_A"))

## End(Not run)

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.