initDispModel: Initialise dispersion 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

initDispModel(matCounts, dfAnnotation, vecConfoundersDisp, scaDFSplinesDisp,
  matWeights, matDispModelInit, lsmatBatchModelInitDisp, strDispModel,
  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.
vecConfoundersDisp	(vector of strings number of confounders on dispersion) [Default NULL] Confounders to correct for in dispersion batch correction model, must be subset of column names of dfAnnotation which describe condounding variables.
scaDFSplinesDisp	(sca) [Default NULL] If strDispModelFull=="splines" or strDispModelRed=="splines", the degrees of freedom of the natural cubic spline to be used as a dispersion parameter model.
matWeights	(numeric matrix cells x mixtures) [Default NULL] Assignments of cells to mixtures (for strMuModel="MM").
matDispModelInit	(numeric matrix genes x disp model parameters) [Default NULL] Contains initialisation of dispersion model parameters according to the used model.
lsmatBatchModelInitDisp	(list) [Default NULL] Initialisation of batch correction models for dispersion parameter.
strDispModel	(str) "constant", "groups", "splines" [Default "constant"] Model according to which dispersion parameter is fit to each gene as a function of population structure in the given model.
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

lsDispModel (list) Initialisation of dispersion model object.

Author(s)

David Sebastian Fischer

See Also

Called by fitModel.

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