evalLogLikMuDispGeneFit: Cost function (zero-inflated) negative binomial model for...

In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

Description

Log likelihood of (zero inflated) negative binomial model. This function is designed to allow numerical optimisation of mean and dispersion paramater model on single gene given the drop-out model.

Usage

evalLogLikMuDispGeneFit(vecTheta, vecCounts, lsMuModelGlobal, lsDispModelGlobal,
  vecTimepoints, vecindTimepointAssign, matDropoutLinModel,
  vecPiConstPredictors, lsDropModelGlobal, vecPiParam = NULL, vecidxNotZero,
  vecidxZero)

Arguments

vecTheta	(numeric vector dispersion (1) and impulse parameters (6)) Dispersion and mean parameter estimates.
vecCounts	(count vector number of cells) Observed read counts, not observed are NA.
lsMuModelGlobal	(list) Object containing meta-data of gene-wise mean parameter models.
lsDispModelGlobal	(list) Object containing meta-data of gene-wise dispersion parameter models.
vecTimepoints	(numerical vector number of unique time coordinates) Unique (pseudo)time coordinates of cells.
vecindTimepointAssign	(numeric vector number samples) Index of time point assigned to cell in list of sorted time points.
matDropoutLinModel	(matrix number of cells x number of predictors) Logistic linear model parameters of the dropout rate as a function of the mean and constant gene-wise coefficients.
vecPiConstPredictors	(numeric vector constant gene-wise coefficients) Constant gene-wise coeffiecients, i.e. predictors which are not the offset and not the mean parameter.
lsDropModelGlobal	(list) Object containing meta-data of cell-wise drop-out parameter models.
vecPiParam	(numeric vector number of observations) Pre-evaluated drop-out model if model is not a function on the mean parameter to be fit.
vecidxNotZero	(index vector vector number of cells) Observation which are larger than zero.
vecidxZero	(index vector number of cells) Observation which are zero.

Value

scaLogLik (scalar) Value of cost function (likelihood) for given gene.

Author(s)

David Sebastian Fischer

YosefLab/LineagePulse documentation built on May 6, 2019, 2:19 p.m.