runDESeq2: Wrapper function for running DESeq2

In YosefLab/ImpulseDE2: Differential expression analysis of longitudinal count data sets

Wrapper function for running DESeq2

Description

Run DESeq2 and extract dispersion parameter estimates. Catch and remove dispersion outlier exception on samples with zero-count observations.

Usage

runDESeq2(dfAnnotationProc, matCountDataProc, boolCaseCtrl, vecConfounders)

Arguments

dfAnnotationProc	(data frame samples x covariates) Sample, Condition, Time (numeric), TimeCateg (str) (and confounding variables if given). Processed annotation table with covariates for each sample.
matCountDataProc	(matrix genes x samples) Read count data.
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 dfAnnotationProc.

Value

(numeric vector length number of genes) Dispersion parameter estimates for each gene. In format of parameter size of dnbinom which is 1/dispersion factor of DESeq2.

Author(s)

David Sebastian Fischer

See Also

Called by runImpulseDE2.

YosefLab/ImpulseDE2 documentation built on Sept. 17, 2022, 2:45 a.m.