Prep TS matrix

Function which prepares and ads the raw count matrix to the timeseries object

The function also differs in the preparation method depending onthe type of differential gene expression method selected (DESeq2 or limma) as this affects the input data. Where DESeq2 (RNAseq data) is stored as individual count file while for limma the function expects a csv file with all samples and genes.

create_raw_count_matrix(
  time_object,
  samp_data,
  path_to_data = NULL,
  limma_id_replace = "GeneName"
)

Arguments

time_object

A timeseries object

samp_data

dataframe containing the sample data

path_to_data

The path towards the count files.

limma_id_replace

The name of gene id's to use from the 'genes' dataframe in the Elist

Value

The time_object, count matrix, and the slot to save it in