load.examples: Retrieving of an example dataset of CytoCompare objects

In tchitchek-lab/CytoCompare: Computational comparisons of cytometry profiles

Description

Downloads and loads an example dataset of CytoCompare objects constructed based on cytometry profiles obtained from healthy human bone marrow unstimulated or stimulated (PMID:21964415).

This example dataset consists on three cytometry profiles of healthy human bone marrow, unstimulated or stimulated by BCR-inductor or IL-7, measured using a mass cytometry panel of more than 30 cell markers. This panel has been designed to identify a large spectrum of immune cell types like monocytes, B, or CD4+ and CD8+ T cells. A SPADE analysis has been performed to identify cell clusters, that have been then manually labelled based on theirs profiles. SPADE cell clusters corresponding to 6 majors cell types have been extracted and a set of rectangle gates have been constructed based these cell types.

Once downloaded, the following objects will be available:
* 'bm_example.cells.b', a 'CELL' object containing the cell profiles of the B cell populations;
* 'bm_example.cells.mono', a 'CELL' object containing the cell profiles of the monocyte cell populations;
* 'bm_example.cells.tCD4naive', a 'CELL' object containing the cell profiles of the naive CD4+ T cell populations;
* 'bm_example.cells.tCD8naive', a 'CELL' object containing the cell profiles of the naive CD8+ T cell populations;
* 'bm_example.cells.tCD4mem', a 'CELL' object containing the cell profiles of the memory CD4+ T cell populations;
* 'bm_example.cells.tCD8mem', a 'CELL' object containing the cell profiles of the memory CD8+ T cell populations;
* 'bm_example.clusters', a 'CLUSTER' object containing the cell cluster profiles for all the different cell populations, identified by SPADE;
* 'bm_example.clusters.b', a 'CLUSTER' object containing the cell cluster profiles of the B cell populations, identified by SPADE;
* 'bm_example.clusters.mono', a 'CLUSTER' object containing the cell cluster profiles of the monocyte cell cluster profiles, identified by SPADE;
* 'bm_example.clusters.tCD4naive', a 'CLUSTER' object containing the cell cluster profiles of the naive CD4+ T cell populations, identified by SPADE;
* 'bm_example.clusters.tCD8naive', a 'CLUSTER' object containing the cell cluster profiles of the naive CD8+ T cell populations, identified by SPADE;
* 'bm_example.clusters.tCD4mem', a 'CLUSTER' object containing the cell cluster profiles of the memory CD4+ T cell populations, identified by SPADE;
* 'bm_example.clusters.tCD8mem', a 'CLUSTER' object containing the cell cluster profiles of the memory CD8+ T cell populations, identified by SPADE;
* 'bm_example.gates', a 'GATE' object containing the gate profiles constructed based on the six main cell populations identified by SPADE;
* 'bm_example.gates.b', a 'GATE' object containing the gate profiles constructed based on the B cell populations;
* 'bm_example.gates.mono', a 'GATE' object containing the gate profiles constructed based on the monocyte cell populations;
* 'bm_example.gates.tCD4naive', a 'GATE' object containing the gate profiles constructed based on the naive CD4T cell populations;
* 'bm_example.gates.tCD8naive', a 'GATE' object containing the gate profiles constructed based on the naive CD8T cell populations;
* 'bm_example.gates.tCD4mem', a 'GATE' object containing the gate profiles constructed based on the memory CD4T cell populations;
* 'bm_example.gates.tCD8mem', a 'GATE' object containing the gate profiles constructed based on the memory CD8T cell populations;
* 'bm_example.mweights', a 'MWEIGHTS' object containing cell markers that can be used in for comparison computations;
* 'bm_example.visne', a list of three 'CELL' objects containing the viSNE cell profiles for each biological sample.

Usage

load.examples(del.file = FALSE)

Arguments

del.file

a logical specifying if the download CytoCompareExample.rdata file must be erased after the loading

Details

This function downloads a CytoCompareExample.rdata file containing the different CytoCompare objects (from a public ftp server "ftp://ftp.cytocompare.org/public/rdata/").

Value

none

tchitchek-lab/CytoCompare documentation built on May 31, 2019, 7:29 a.m.