tof_batch_correct: Perform groupwise linear rescaling of high-dimensional...

In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

Perform groupwise linear rescaling of high-dimensional cytometry measurements

Description

This function performs quantile normalization on high-dimensional cytometry data in tidy format using either linear rescaling or quantile normalization. Each channel specified by 'channel_cols' is batch corrected, and 'group_cols' can be used to break cells into groups for which the batch correction should be performed separately.

Usage

tof_batch_correct(
  tof_tibble,
  channel_cols,
  group_cols,
  augment = TRUE,
  method = c("rescale", "quantile")
)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
channel_cols	Unquoted column names representing columns that contain single-cell protein measurements. Supports tidyselect helpers.
group_cols	Optional. Unquoted column names indicating which columns should be used to group cells before batch correction. Batch correction is then performed independently within each group. Supports tidyselect helpers.
augment	A boolean value indicating if the output should replace the 'channel_cols' in 'tof_tibble' with the new, batch corrected columns (TRUE, the default) or if it should only return the batch-corrected columns (FALSE) with all other columns omitted.
method	A string indicating which batch correction method should be used. Valid options are "rescale" for linear scaling (the default) and "quantile" for quantile normalization using normalize.quantiles.

Value

If augment = TRUE, a tibble with the same number of rows and columns as tof_tibble, with the columns specified by 'channel_cols' batch-corrected. If augment = FALSE, a tibble containing only the batch-corrected 'channel_cols'.

Examples

NULL

keyes-timothy/tidytof documentation built on March 31, 2024, 12:01 p.m.