importResultsFromSPADE: Importation of clustering results generated by SPADE

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

Importation of clustering results generated by SPADE

Description

The 'importResultsFromSPADE()' function imports SPADE cell clustering results from a specified path. This function imports the cluster phenotype matrix and count matrix as well as the SPADE tree. This function apply an hyperbolic sine transformation to imported FCS data (unless 'trans' = log or none) and compute the marker range quantiles.

Usage

importResultsFromSPADE(path, exclude.markers = c("cell_length",
  "FileNum", "density", "time"), probs = c(0.05, 0.95),
  trans = "arcsinh", quantile.approximation = FALSE,
  th.min_cells = 0, load.phenotype = TRUE, assignments = NULL)

Arguments

path	a character specify the path of SPADE results folder
exclude.markers	a character vector of markers to exclude (case insensitive)
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)
th.min_cells	a numeric specifying the minimum number of cell in a cluster of a sample to take its phenotype in account
load.phenotype	a logical specifying if the phenotype matrix and fcs file will be loaded
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', '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.

Value

a S4 object of class 'Results'

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