log2se: calculate the log2 transformed ratios for...

In jianhong/NADfinder: Call wide peaks for sequencing data

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")

jianhong/NADfinder documentation built on Nov. 2, 2024, 12:09 a.m.