data {CATALYST} | 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)

[Package CATALYST version 1.14.1 Index]