scoreSummarizedExperiment {ORFik} | R Documentation

## Helper function for makeSummarizedExperimentFromBam

### Description

If txdb or gtf path is added, it is a rangedSummerizedExperiment For FPKM values, DESeq2::fpkm(robust = FALSE) is used

### Usage

    scoreSummarizedExperiment(
      final,
      score = "transcriptNormalized",
      collapse = FALSE
    )

### Arguments

`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)

### Value

a DEseq summerizedExperiment object (transcriptNormalized) or matrix (if fpkm input)

[Package ORFik version 1.12.13 Index]