scoreSummarizedExperiment: Helper function for makeSummarizedExperimentFromBam

In JokingHero/ORFik: Open Reading Frames in Genomics

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)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.