Merge locations of peak and valley landmarks

This function merges the peak and valley landmarks locations and fills in NA if the landmark is not detected.

landmark_fill_na(
  peak_landmark_list = NULL,
  valley_landmark_list = NULL,
  landmark_align_type = NULL,
  midpoint_type = "valley",
  neg_candidate_thres = asinh(10/5 + 1)
)

Arguments

peak_landmark_list

Matrix of peak landmark detection results. Rows are samples, and column(s) are the peak locations.

valley_landmark_list

Matrix of valley landmark detection results. Rows are samples, and column(s) are the valley locations.

landmark_align_type

Algin the peak and valleys using one of the "negPeak", "negPeak_valley", "negPeak_valley_posPeak", and "valley" alignment modes.

midpoint_type

Fill in the missing first valley by the midpoint of two positive peaks ("midpoint") or impute by other valleys ("valley").

neg_candidate_thres

The upper bound for the negative peak. Users can refer to their IgG samples to obtain the minimal upper bound of the IgG sample peak. It can be one of the values of asinh(4/5+1), asinh(6/5+1), or asinh(8/5+1) if the right 95% quantile of IgG samples is large.

Examples

if (FALSE) {
landmark_fill_na(
  peak_landmark_list = peak_landmark_list,
  valley_landmark_list = valley_landmark_list,
  landmark_align_type = "negPeak_valley_posPeak"
)
}