initDispModel: Initialise dispersion model container object

Description Usage Arguments Value Author(s) See Also

View source: R/srcLineagePulse_initialiseDispModel.R

Description

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

Usage

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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.


LineagePulse documentation built on Nov. 8, 2020, 7:01 p.m.