normalise_data: normalise_data contains all the functions to normalise...

In mtrussart/CytofRUV: CytofRUV for analysing multiple CyTOF batches

normalise_data contains all the functions to normalise several Cytof datasets by removing the unwanted variation between datasets arising from experimental artefacts.

Description

normalise_data

contains all the functions to normalise several Cytof datasets by removing the unwanted variation between datasets arising from experimental artefacts.

Usage

normalise_data(
  data,
  raw_data,
  rep_samples,
  norm_clusters,
  k,
  num_clusters,
  wd_data,
  dir_norm_data,
  other_markers_fcs_file = NULL
)

Arguments

data	Datasets before normalisation
raw_data	Raw data
rep_samples	Replicated samples
norm_clusters	Clusters to be normalised
k	Dimension of the unwanted variation
num_clusters	Total number of clusters
wd_data	Path to the directory containing all raw fcs files, the metadata file and the panel file
dir_norm_data	Directory name containing all norm fcs files, the metadata file and the panel file
other_markers_fcs_file	Optional to add more markers to be saved in the .fcs file not normalised

Value

Normalised metadata file

mtrussart/CytofRUV documentation built on Aug. 3, 2022, 2:28 a.m.