processData {ImpulseDE2}R Documentation

Check and process input to runImpulseDE2()

Description

Check validity of input and process count data matrix and annotation into data structures used later in runImpulseDE2. processData is structure in the following way:

Usage

processData(dfAnnotation, matCountData, boolCaseCtrl, vecConfounders,
  vecDispersionsExternal, vecSizeFactorsExternal)

Arguments

dfAnnotation

(data frame samples x covariates) Sample, Condition, Time (numeric), TimeCateg (str) (and confounding variables if given). Annotation table with covariates for each sample.

matCountData

(matrix genes x samples) [Default NULL] Read count data, unobserved entries are NA.

boolCaseCtrl

(bool) Whether to perform case-control analysis. Does case-only analysis if FALSE.

vecConfounders

(vector of strings number of confounding variables) Factors to correct for during batch correction. Have to supply dispersion factors if more than one is supplied. Names refer to columns in dfAnnotation.

vecDispersionsExternal

(vector length number of genes in matCountData) [Default NULL] Externally generated list of gene-wise dispersion factors which overides DESeq2 generated dispersion factors.

vecSizeFactorsExternal

(vector length number of cells in matCountData) [Default NULL] Externally generated list of size factors which override size factor computation in ImpulseDE2.

Value

(list length 4)

Author(s)

David Sebastian Fischer

See Also

Called by runImpulseDE2.


[Package ImpulseDE2 version 1.10.0 Index]