log2se {NADfinder} | R Documentation

## calculate the log2 transformed ratios for SummarizedExperiment class

### Description

Calculate the log2 transformed ratios for nucleolus vs genome. pseudo-count will be used to avoid x/0 or log(0).

### Usage

    log2se(
      se,
      nucleolusCols,
      genomeCols,
      pseudocount = 1L,
      transformation = c("log2OddsRatio", "log2CPMRatio", "log2Ratio"),
      chrom.level.lib = TRUE
    )

### Arguments

`se` | A RangedSummarizedExperiment object. The output of tileCount.
`nucleolusCols, genomeCols` | column Names of counts for nucleolus and genome. They should be the column names in the assays of se. Ratios will be calculated as log2(transformed nucleolusCols/transformed genomeCols).
`pseudocount` | default to 1, pseudo-count used to aviod x/0 or log(0).
`transformation` | transformation type
`chrom.level.lib` | indicating whether calculating CPM or odds using sequence depth of the whole genome or the corresponding chromosome

### Value

A RangedSummarizedExperiment object with log2 transformed ratios. Assays will be named as nucleolus, genome and ratio.

### Author(s)

Jianhong Ou and Julie Zhu

### Examples

    library(SummarizedExperiment)
    se <- SummarizedExperiment(assays=list(counts=DataFrame(A=seq_len(3),
           B=rep(1, 3), C=rep(4, 3), D=rep(2, 3))),
                      rowRanges=GRanges(c("chr1","chr1", "chr2"),
                          IRanges(c(1, 10, 20),
                                width=9)))
    metadata(se)$lib.size.chrom <- data.frame( c(1000, 1000), c(2000, 2000), c(200,200), c(300,300))
    colnames(metadata(se)$lib.size.chrom) <- c("A", "B", "C", "D")
    rownames(metadata(se)$lib.size.chrom) <- c("chr1", "chr2")
    log2se(se, nucleolusCols = c("A", "C"), genomeCols = c("B", "D"), transformation = "log2Ratio")
    log2se(se, nucleolusCols = c("A", "C"), genomeCols = c("B", "D"), transformation = "log2CPMRatio")
    log2se(se, nucleolusCols = c("A", "C"), genomeCols = c("B", "D"),
        transformation = "log2OddsRatio")

[Package NADfinder version 1.18.0 Index]