Normalize with DESeq2 — normalize_timeSeries_with

Function which normalizes the raw count matrix from a timeseries object using the DESeq2 normalization.

normalize_timeSeries_with_deseq2(
  time_object,
  controlGenes = NULL,
  use_batch = FALSE,
  no_condition = FALSE
)

Arguments

time_object: The time object with the normalized count matrix included, as well as the DESeq2 object
controlGenes: The controlGenes parameter to be passed to DESeq's estimateSizeFactors function. It allows to normalize on specific identifiers.
use_batch: whether or not to add the batch effect to the DESeq2 design. This requires a 'batch' column to be present in the sample file
no_condition: Boolean incating if the analysis contains no case-control. This indicates that the normalization will be performed exclusively on a timepoint perspective.

The timeseries object with the added normalized count matrix

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