data: Example data sets
In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

data	R Documentation

Example data sets

Description

Concatenation & Normalization

raw_data

a flowSet with 3 experiments, each containing 2'500 raw measurements with a variation of signal over time. Samples were mixed with DVS beads capture by mass channels 140, 151, 153, 165 and 175.
Debarcoding

sample_ff

a flowFrame following a 6-choose-3 barcoding scheme where mass channels 102, 104, 105, 106, 108, and 110 were used for labeling such that each of the 20 individual barcodes are positive for exactly 3 out of the 6 barcode channels.

sample_key

a data.frame of dimension 20 x 6 with sample names as row and barcode masses as column names. Contains a binary code of length 6 for each sample in sample_ff, e.g. 111000, as its unique identifier.
Compensation

ss_exp

a flowFrame with 20'000 events. Contains 36 single-antibody stained controls where beads were stained with antibodies captured by mass channels 139, 141 through 156, and 158 through 176, respectively, and pooled together.

mp_cells

a flowFrame with 5000 spill-affected multiplexed cells and 39 measurement parameters.

isotope_list

a named list of isotopic compositions for all elements within 75 through 209 u corresponding to the CyTOF mass range at the time of writing.
Differential Analysis

PBMC_fs

a flowSet with PBMCs samples from 6 patients. For each sample, the expression of 10 cell surface and 14 signaling markers was measured before (REF) and upon BCR/FcR-XL stimulation (BCRXL) with B cell receptor/ Fc receptor crosslinking for 30', resulting in a total of 12 samples.

PBMC_panel

a 2 column data.frame that contains each marker's column name in the FCS file, and its targeted protein marker.

PBMC_md

a data.frame where each row corresponds to a sample, and with columns describing the experimental design.

merging_table

a 20 x 2 table with "old_cluster" IDs and "new_cluster" labels to exemplify manual cluster merging and cluster annotation.

Value

see descriptions above.

Author(s)

Helena L Crowell helena.crowell@uzh.ch

References

Bodenmiller, B., Zunder, E.R., Finck, R., et al. (2012). Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nature Biotechnology 30(9): 858-67.

Coursey, J.S., Schwab, D.J., Tsai, J.J., Dragoset, R.A. (2015). Atomic weights and isotopic compositions, (available at http://physics.nist.gov/Comp).

Examples

### example data for concatenation & normalization:
    # raw measurement data
    data(raw_data)
  
### example data for debarcoding:
    # 20 barcoded samples
    data(sample_ff)
    # 6-choose-3 barcoding scheme
    data(sample_key)

### example data for compensation:
    # single-stained control samples
    data(ss_exp)
    # multiplexed cells
    data(mp_cells)
    
### example data for differential analysis:
    # REF vs. BCRXL samples
    data(PBMC_fs)
    # antigen panel & experimental design
    data(PBMC_panel, PBMC_md)
    # exemplary manual merging table
    data(merging_table)

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.