importResultsFromCLR.ACS: Importation of clustering results from a folder containing...

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Importation of clustering results from a folder containing ACS files

Description

The 'importResultsFromCLR.ACS()' function imports cell clustering results from CLR files contained in a specified folder. CLR files must be in ACS format. This function imports the cluster phenotype and abundance.

Usage

importResultsFromCLR.ACS(path, prob.th = 0.8, th.min_cells = 0,
  probs = c(0.05, 0.95), trans = "arcsinh",
  quantile.approximation = FALSE, exclude.markers = NULL,
  assignments = NULL)

Arguments

path	a character specify the path of the ACS CLR files
prob.th	a numeric specifying the probability threshold to use for considering considering the cluster of each each cells
th.min_cells	a numeric specifying the minimum number of cell in a cluster of a sample to take its phenotype in account
probs	a vector of probabilities with 2 values in [0,1] to compute marker range quantiles. First is the lower bound and second is the upper bound.
trans	a character specifying what transformation ("arcsinh", "logicle", or "none") will be applied on the cluster expression matrix ("arcsinh" by default)
quantile.approximation	a logical specifying if marker range quantiles are computed using all cells (FALSE), or is the means of the quantile of each samples (TRUE)
exclude.markers	a character vector of markers to exclude (case insensitive)
assignments	a data.frame containing all samples names (in rownames) and columns providing contextual associations like "bc" (biological conditions), "tp" (biological conditions) and "ind" (individuals)

Details

This function returns a 'Results' object including 'flowset', 'fcs.files' slots but not 'graph' and 'graph.layout' slots. The computation of marker range quantiles can be approximated using 'quantile.approximation' parameter which is more efficient in term of loading time and memory usage. The name of each file will be used as the name of the sample. All FCS files corresponding to all the samples must be contained in a single folder.

For each cell, the selected cluster will be one having the greater probability higher than the 'prob.th' parameter.

Value

a S4 object of class 'Results'

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.