importResultsFromTables: Importation of clustering results from text files

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

Importation of clustering results from text files

Description

The 'importResultsFromTables()' function imports cell clustering results from two dataframes ('cluster.abundances' and 'cluster.phenotypes'). This function returns a 'Results' object.

Usage

importResultsFromTables(cluster.abundances, cluster.phenotypes,
  clustering.markers = NULL, th.min_cells = 0, assignments = NULL)

Arguments

cluster.abundances	a dataframe of cells abundances with clusters in row and samples in column
cluster.phenotypes	a dataframe containing median marker expression values for each cluster of each sample. In additions of markers, the two first columns are are dedicated to "cluster" and "sample" identifiers.
clustering.markers	a character vector specifying markers that have been used during the clustering procedure (if NULL, all markers will be considered as clustering markers)
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 without 'flowset', 'fcs.files', 'graph' and 'graph.layout' slots.

The 'cluster.abundances' dataframe must be formatted with the cluster names in rownames as following:

x	sample1	sample2	sample3	...
cluster1	749	5421	8424	...
cluster2	450	412	614	...
cluster3	288	782	478	...
...	...	...	...	...

The 'cluster.phenotypes' dataframe must be formatted as following:

sample	cluster	marker1	marker2	marker3	...
sample1	cluster1	0.212	0.445	1.756	...
sample1	cluster3	0.434	0.785	0.654	...
sample2	cluster1	0.574	2.641	3.854	...
sample2	cluster2	1.454	1.755	-0.568	...
sample2	cluster3	1.445	1.875	-0.786	...
sample3	cluster1	0.157	2.121	1.648	...
sample3	cluster2	1.415	1.963	0.786	...
sample3	cluster3	1.275	1.427	0.754	...
...	...	...	...	...	...

Value

a S4 object of class 'Results'

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