estimateImpulseParam: Compute peak and valley impulse model parameter...

In YosefLab/ImpulseDE2: Differential expression analysis of longitudinal count data sets

Compute peak and valley impulse model parameter initialisations for data of one gene

Description

[Model fitting function hierarchy: helper to level 3 out of 4] This is a fitting helper function which computes parameter intialisations and does not wrap or execute numerical optimisation. The peak model models a maximum between start and end time, the valley model models a minimum between start and end time.

Usage

estimateImpulseParam(vecCounts, vecTimepoints, vecSizeFactors,
  lsvecidxBatch)

Arguments

vecCounts	(numeric vector number of samples) Read count data.
vecTimepoints	(numeric vector length number of samples) Time coordinates of each sample.
vecSizeFactors	(numeric vector number of samples) Model scaling factors for each sample which take sequencing depth into account (size factors).
lsvecidxBatch	(list length number of confounding variables) List of index vectors. One vector per confounding variable. Each vector has one entry per sample with the index batch within the given confounding variable of the given sample. Batches are enumerated from 1 to number of batches.

Value

(list length 2)

• peak (numeric vector length 6) {beta, h0, h1, h2, t1, t2} Peak model initialisations of impulse model parameters.

• valley (numeric vector length 6) {beta, h0, h1, h2, t1, t2} Valley model initialisations of impulse model parameters.

Author(s)

David Sebastian Fischer

See Also

Called by fitConstImpulseGene.

YosefLab/ImpulseDE2 documentation built on Sept. 17, 2022, 2:45 a.m.