Create conditional DE results — conditional_DE

A wrapper function which performs conditional differential gene expression analysis for every timepoint in the timeseries object

Conditional differential gene expression experiments involves the comparison of the experiment vs the control. This is done at every timepoint.

The function calls the necessary sub functions for the differential expression analysis based on the type needed (DESeq2 for RNAseq or limma for microarray)

conditional_DE_wrapper(time_object, vignette_run = FALSE)

Arguments

time_object: A timeseries object containing a DESeq2_obj
vignette_run: Boolean indicating if a run is for vignettes or not.

Value

The timeseries object with the conitional differential expression results added to the DE_results slot of the object.

Examples

TS_object<-create_example_object_for_R()
TS_object<-normalize_timeSeries_with_deseq2(time_object=TS_object)
#> converting counts to integer mode
TS_object<-conditional_DE_wrapper(TS_object,vignette_run=TRUE)