pwl_after_dewarping: Piecewise linear warping after aligning the landmarks

In zhenkewu/spotgear: Subset Profiling and Organizing Tools for Gel Electrophoresis Autoradiography in R

Description

Because at the right side of the gel, we have few peaks, data contain few information about the dewarping function. We downsample the gel, so that we only need to consider the dewarping results on the J=50 landmarks' dewarping results. NB: assumed that all gels have 19 non-reference lanes. Need to change otherwise.

Usage

pwl_after_dewarping(g_id, l_id, normalized_rf, dat_without_lane1,
  data_lcm_all, zero_to_one_v_landmark, bugs_gel_id, bugs_in_gel_id,
  N_per_gel, Z_map, n_vec, lookup)

Arguments

g_id	Gel id
l_id	Lane id
normalized_rf	The normalized_rf that is between 0 and 1. Note this subtle change compared after cropping the right end of the gel.
dat_without_lane1	The data frame without peaks obtained from the reference lanes. Because when doing warping, we know these reference molecules do not exactly correspond to the molecules that would be observed in the serum samples.
data_lcm_all	A binary matrix of the number of rows being the number of serum samples and the number of columns being J+2 (J for intermediate landmarks and 2 end points)
zero_to_one_v_landmark	The landmark location on the zero to one scale.
bugs_gel_id	Starts from 1.
bugs_in_gel_id	Starts from 1 to say 19.
N_per_gel	Analyzed number of lanes per gel.
Z_map	a vector of length equal to total number of peaks detected; each element represents the landmark a peak is aligned to
n_vec	A vector of length equal to the total lane number; each element is the number of peaks within a lane.
lookup	A matrix with no. of rows equal to sample size, no. of columns equal to maximum number of peaks per lane. The numbers indicate the no. of peaks appearing from all the lanes.

Value

A list of two elements:

• ref_index Among normalized_rf, the index of the one that is closest to each of the peak-matched landmarks. Because we want to use these index as anchors to do piecewise linear warping.

• warped_ind Warping mapping: bin index for post-dewarping data |-> bin index for the pre-dewarping data.

zhenkewu/spotgear documentation built on June 22, 2019, 1:55 a.m.