prep.cytonorm: prep.cytonorm - Prepare reference data into a FlowSOM object

In sydneycytometry/Spectre: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data.

Description

This function allows you to prepare reference data ahead of performing batch alignment.

Usage

prep.cytonorm()

Arguments

dat	NO DEFAULT. A data.table consisting of the 'refernece' data you will use to train the alignment algorithm
cellular.cols	NO DEFAULT. A vector of column names from the data.table that contain 'cellular' markers
cluster.cols	NO DEFAULT. A vector of column names from the data.table that contain markers you wish to use for clusteirng
batch.col	NO DEFAULT. Name of the column that contains batch names
sample.col	DEFAULT = NULL. Name of the column that contains sample names
dir	DEFAULT = getwd(). Sets the working directory to operate from. Because this function involves some reading/writing of files, it's best to set this to somewhere static in case the active working directory moves to a subfolder, and then doesn't return because the function runs into an error.
xdim	DEFAULT = 5. Size of X-axis of FlowSOM grid.
ydim	DEFAULT = 5. Size of Y-axis of FlowSOM grid.
meta.k	DEFAULT = 10. Number of metaclusters. If set to 1, will map all cells to a single metacluster
seed	DEFAULT = 42. Seed for reproducibility.
mem.ctrl	DEFAULT = TRUE. Allows the function to clear held memory on occasion.

Value

Returns an object which represents the alignment model. In this preparation stage, it contains the FlowSOM object containing the reference data. The 'train.align' function can then be used to calculate the conversions between batches for each metacluser.

Author(s)

Thomas M Ashhurst, [e-mail]

References

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

Examples

align.model <- prep.cytonorm()

sydneycytometry/Spectre documentation built on March 20, 2021, 2:15 a.m.