importResultsFromCLR.CSV: 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 CVS files

Description

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

Usage

importResultsFromCLR.CSV(path, prob.th = 0.8, th.min_cells = 0,
  assignments = NULL)

Arguments

path	a character specify the path of the CVS 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
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 with only cluster abundance information (no phenotype). The name of each file will be used as the name of the sample.

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.