scoreSummarizedExperiment {ORFik} | R Documentation |
If txdb or gtf path is added, it is a rangedSummerizedExperiment For FPKM values, DESeq2::fpkm(robust = FALSE) is used
scoreSummarizedExperiment( final, score = "transcriptNormalized", collapse = FALSE )
final |
ranged summarized experiment object |
score |
default: "transcriptNormalized" (row normalized raw counts matrix), alternative is "fpkm", "log2fpkm" or "log10fpkm" |
collapse |
a logical/character (default FALSE), if TRUE all samples within the group SAMPLE will be collapsed to one. If "all", all groups will be merged into 1 column called merged_all. Collapse is defined as rowSum(elements_per_group) / ncol(elements_per_group) |
a DEseq summerizedExperiment object (transcriptNormalized) or matrix (if fpkm input)