deg analysis function template

deg_template.R

#################

counts1
counts2
counts3


analyse_DEG <- function(dataset, hpi){
    #0 pre-filter sample table
    sampletable <- SampleTable %>%
                    select(timepoint == hpi)
    
    #1 prepare ddsmat object
    ddsmat <- DESeqDataSetFromMatrix(countData = dataset,
                                     colData = sampletable,
                                     design = ~ treatment)
    #2 filter low count out
    ddsmat <- ddsmat[ rowSums(counts(ddsmat)) > 1, ]
    
    #3 dif expression analysis
    dds <- DESeq(ddsmat)
    
    #4 result genes in df format
    resdf <- as.tibble(results(dds))
    
    #5 filter df with results
    
    #6 do smth else ...
    
    }

### calling function:
res_14 <- analyse_DEG(counts1, '14_hpi')
res_24 <- analyse_DEG(counts2, '24_hpi')