initMuModel: Initialise mean model container object

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

Description

Either use supplied fits from previous fitting or initialise from count data.

Usage

initMuModel(matCounts, dfAnnotation, vecConfoundersMu, vecNormConst,
  scaDFSplinesMu, matWeights, matMuModelInit, lsmatBatchModelInitMu, strMuModel,
  MAXIT_BFGS_MuDisp, RELTOL_BFGS_MuDisp)

Arguments

matCounts	(matrix genes x cells) Count data of all cells, unobserved entries are NA.
dfAnnotation	(data frame cells x meta characteristics) Annotation table which contains meta data on cells.
vecConfoundersMu	(vector of strings number of confounders on mean) [Default NULL] Confounders to correct for in mu batch correction model, must be subset of column names of dfAnnotation which describe condounding variables.
vecNormConst	(numeric vector number of cells) Model scaling factors, one per cell. These factors linearly scale the mean model for evaluation of the loglikelihood.
scaDFSplinesMu	(sca) [Default NULL] If strMuModel=="splines", the degrees of freedom of the natural cubic spline to be used as a mean parameter model.
matWeights	(numeric matrix cells x mixtures) [Default NULL] Assignments of cells to mixtures (for strMuModel="MM").
matMuModelInit	(numeric matrix genes x mu model parameters) [Default NULL] Contains initialisation of mean model parameters according to the used model.
lsmatBatchModelInitMu	(list) [Default NULL] Initialisation of batch correction models for mean parameter.
strMuModel	(str) "constant", "groups", "MM", "splines","impulse" [Default "impulse"] Model according to which the mean parameter is fit to each gene as a function of population structure in the alternative model (H1).
MAXIT_BFGS_MuDisp	(sca) Maximum number of iterations in BFGS estimation of Mu/Disp models. This is a control parameter to optim().
RELTOL_BFGS_MuDisp	(sca) Relative tolerance of BFGS estimation of Mu/Disp models. This is a control parameter to optim().

Value

lsMuModel (list) Initialisation of mean model object.

Author(s)

David Sebastian Fischer

See Also

Called by fitModel.

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