runCITRUS: Run CITRUS

In Mamie/mwang: Collection of useful functions

Description

Run CITRUS on selected channels

Usage

runCITRUS(dataDir, selected.desc, fileList = NULL,
  family = "classification", transformCofactor = 5,
  minClusterSizePercent = 0.05, fileSampleSize = 1000, nFolds = 1,
  featureType = c("abundances"), seed = 1, pattern = "fcs",
  labels = NULL)

Arguments

dataDir	Full path to the folder containing FCS files.
selected.desc	A character vector of selected channel description.
fileList	A list of full path to FCS files.
family	A character scalar of model type.
transformCofactor	An integer for arcsinh transform channel; default 5
fileSampleSize	The number of cells subsampled from each file.
nFolds	Number of folds used for clustering
featureType	A character vector of feature type (abundances, proportion).
seed	A seed to reproduce the run.
pattern	Regular expression used to select FCS files in the folder.
labels	Optional vector of label used for balancing clustering folds
minimumClusterSizePercent	Minimal size of cluster in proportion.

Value

A list consisting of feature matrix, citrus clustering object and combinedFCSSet object.

Mamie/mwang documentation built on May 14, 2019, 7:15 p.m.