do.prep.fsom: do.prep.fsom - Function to prepare a FlowSOM (fsom) object...

In tomashhurst/Spectre: A Toolbox for the Analysis of High-Dimensional Cytometry and Single-Cell Data

Description

This function allows you to prepare a FlowSOM (fsom) object for alignment with CytoNorm.

Usage

do.prep.fsom(dat, use.cols, sample.col, xdim, ydim, nClus, nCells, scale, seed)

Arguments

dat	NO DEFAULT. data.table of the dataset you wish to run in FlowSOM.
use.cols	NO DEFAULT. Vector of character etnries. Columns to use to calculate FlowSOM.
sample.col	NO DEFAULT. Character, name of the column denoting samples
xdim	DEFAULT = 5. Size of Y-axis of FlowSOM grid.
nClus	DEFAULT = 10. Number of metaclusters. If set to 1, will map all cells to a single metacluster
nCells	DEFAULT = NULL. Number of cells to downsample to, otherwise 'NULL' will use all available cells
scale	DEFAULT = FALSE. Do features need to be scaled?
seed	DEFAULT = 42. Seed for reproducibility.

Value

Returns a FlowSOM object.

Author(s)

Thomas M Ashhurst, [e-mail]

References

Ashhurst, T. M., et al. (2019). https://www.ncbi.nlm.nih.gov/pubmed/31077106

Examples

ref.fsom <- do.prep.fsom()

tomashhurst/Spectre documentation built on Dec. 23, 2021, 11:55 a.m.