Skip to contents

Batch-correct a tibble of high-dimensional cytometry data using quantile normalization.

Source: R/batch_correction.R
tof_batch_correct_quantile.Rd

This function performs quantile normalization on high-dimensional cytometry data in tidy format using normalize.quantiles. Optionally, groups can be specified and normalized separately.

Usage

tof_batch_correct_quantile(
  tof_tibble,
  channel_cols,
  group_cols,
  augment = TRUE
)

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.

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
#> NULL