Wrapper function which performs the temporal differential gene expression analyses
The temporal differential analyses is the comparison of each timepoint irrelevant of their conition (experiment or control). Timepoints are compared with the next immediate timepoint. For example, if there are three timepoints, two temporal differential gene expressions will be performed: TP2 vs TP1 and TP3 vs TP2.
The function subsets the DESeq2_obj based on the necessary samples and adjusts the condition of the object to reflect the comparison being done
temporal_DE_wrapper(
time_object,
do_all_combinations = FALSE,
vignette_run = FALSE
)A timeseries object containing a DESeq2_obj
Allows for all temporal combinations to be done instead of just sequential comparison. ex: do TP2vsTP1, TP3vsTP2, AND TP3vsTP1. In a normal instance only the first two comparison of the example would be run.
Boolean indicating if a run is for vignettes or not.
The timeseries object with the temporal differential expression results added to the DE_results slot of the object.
TS_object<-create_example_object_for_R()
TS_object<-normalize_timeSeries_with_deseq2(time_object=TS_object)
#> converting counts to integer mode
TS_object<-temporal_DE_wrapper(TS_object,do_all_combinations=TRUE,vignette_run=TRUE)