estimateSigmoidParam: Compute up and down sigmoid model parameter initialisations...

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

Compute up and down sigmoid model parameter initialisations for data of one gene

Description

[Model fitting function hierarchy: helper to level 2 out of 3] This is a fitting helper function which computes parameter intialisations and does not wrap or execute numerical optimisation. The up model models a sigmoidal expression increase over time, the down model a sigmoidal decrease over time.

Usage

estimateSigmoidParam(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, t} Up model initialisations of sigmoidal model parameters.

• valley (numeric vector length 6) {beta, h0, h1, t} Down model initialisations of sigmoidal model parameters.

Author(s)

David Sebastian Fischer

See Also

Called by fitSigmoidGene.

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