Align the peak and valley landmarks by the warpset function

Source: R/peak_alignment.R

This function monotonously transforms the ADT marker counts to align the landmarks detected in previous steps. By aligning the landmarks, ADTnorm removes the batch effect and allows integration across batches/studies.

peak_alignment(
  cell_x_adt,
  cell_x_feature = NULL,
  landmark_matrix = NULL,
  target_landmark = NULL
)

Arguments

cell_x_adt

Matrix of ADT raw counts in cells (rows) by ADT markers (columns) format.

cell_x_feature

Matrix of cells (rows) by cell features (columns) such as cell type, sample, and batch-related information.

landmark_matrix

Matrix of peak and valley landmarks after filling in NA using the landmark_fill_na function.

target_landmark

Leave it as NULL to align the landmark to the mean location across samples. Denote it by a vector of the same length as the column number of the landmark to align the negative peak, valley, and positive peak(s) to the specified fixed location.

Examples

if (FALSE) {
peak_alignment(cell_x_adt, cell_x_feature, landmark_matrix)
}