run.ruv: run.ruv - Run the the CytofRUV alignment method.

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 run the CytofRUV alignment method.

Usage

run.align()

Arguments

dat	NO DEFAULT.A data.table consisting of the data (both reference and taret) you wish to align
sample.col	NO DEFAULT. Column name of the data.table that contains sample names
batch.col	NO DEFAULT. Column name of the data.table that contains batch labels
align.cols	NO DEFAULT. Vector of column names to align.
ref.samples	NO DEFAULT. Character vector of sample names that are used as reference data.
cluster.col	DEFAULT = NULL. Column name of the data.table that contains clusters. If NULL, will align data without clusters.
k	DEFAULT = K. K value for alignment
dir	DEFAULT = getwd(). Directory where the work is being done
append.name	DEFAULT = '_ruv'. Text to be appended to end of each new column containing aligned data

Value

Returns a data.table with aligned data added in new columns.

Author(s)

Thomas M Ashhurst, [e-mail]

References

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

Examples

cell.dat <- run.ruv()

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