Remove Batch Effect from Cluster Hits — remove_batch_effect_cluster

This function removes batch effects from the data for each level specified by the condition. It supports both isolated and integrated modes, with optional handling for a second batch column.

Usage

remove_batch_effect_cluster_hits(
  data,
  meta,
  condition,
  meta_batch_column,
  meta_batch2_column,
  design,
  mode,
  spline_params
)

Arguments

data: A dataframe containing the main data.
meta: A dataframe containing meta information.
condition: A string specifying the column in `meta` that divides the experiment into levels.
meta_batch_column: A string specifying the column in `meta` that indicates batch information.
meta_batch2_column: A string specifying the second batch column in `meta`, if applicable.
design: A design matrix for the experiment.
mode: A string indicating the mode of operation: "isolated" or "integrated".
spline_params: A list of spline parameters for the design matrix.

Value

A list of dataframes with batch effects removed for each level.

Details

The function operates in two modes:

isolated: Processes each level independently, using only data from that level.
integrated: Processes the entire dataset together.

If `meta_batch_column` is specified, the function removes batch effects using `removeBatchEffect`. If a second batch column (`meta_batch2_column`) is specified, it is also included in the batch effect removal.