Perform groupwise linear rescaling of high-dimensional cytometry measurements
Source:R/batch_correction.R
tof_batch_correct.RdThis 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.