transformData {NADfinder} | R Documentation

## transform counts to log2 cpm ratios, log2 ratios or log2 odds ratios

### Description

calculate the log2 ratios, log2 cpm (count per million) ratios, or log2 odds ratios for nucleolus vs genome. pseudo-count will be used to avoid x/0 or log(0).

### Usage

    transformData(
      A,
      B,
      seqnames.A,
      seqnames.B,
      pseudo.count = 1L,
      transformation = c("log2OddsRatio", "log2CPMRatio", "log2Ratio"),
      chrom.level.lib = TRUE,
      lib.size.A,
      lib.size.B
    )

### Arguments

`A, B` | window-level counts for nucleolus and genome, extracted from the assays of the output of the tileCounts function
`seqnames.A, seqnames.B` | seqnames, extracted from the rowRanges of the ouput of the tileCounts function
`pseudo.count` | pseudo-count will be used to aviod x/0 or log0, defult to 1.
`transformation` | transformation type
`chrom.level.lib` | indicating whether calculating CPM or odds using sequence depth of the whole genome or the corresponding chromosome
`lib.size.A, lib.size.B` | library size for A and B. these two dataframes contain chromosome-level sequence depth for the chromosomes, which can be extracted from the metadata of the output of the tileCounts function

### Value

a numeric vector of log2 ratios, log2 CPM ratios or log2 odds ratios.

### Author(s)

Julie Zhu

### Examples

    transformData(seq_len(10), 10:1, seqnames.A = Rle(c("chr1", "chr2" ) , c(5,5)),
    Rle(c("chr1", "chr2" ) , c(5,5)), transformation = "log2OddsRatio",
    chrom.level.lib = FALSE, lib.size.A = cbind(c("chr1", "chr2"), c(10000, 12000)),
    lib.size.B = cbind(c("chr1", "chr2"), c(10000, 12000)))
    transformData(seq_len(10), 10:1, seqnames.A = Rle(c("chr1", "chr2" ) , c(5,5)),
    Rle(c("chr1", "chr2" ) , c(5,5)), transformation = "log2CPMRatio",
    chrom.level.lib = FALSE, lib.size.A = cbind(c("chr1", "chr2"), c(10000, 12000)),
    lib.size.B = cbind(c("chr1", "chr2"), c(10000, 12000)))
    transformData(seq_len(10), 10:1, seqnames.A = Rle(c("chr1", "chr2" ) , c(5,5)),
    Rle(c("chr1", "chr2" ) , c(5,5)), transformation = "log2CPMRatio",
    chrom.level.lib = TRUE, lib.size.A = cbind(c("chr1", "chr2"), c(100, 12000)),
    lib.size.B = cbind(c("chr1", "chr2"), c(10000, 200)))
    transformData(seq_len(10), 10:1, seqnames.A = Rle(c("chr1", "chr2" ) , c(5,5)),
    Rle(c("chr1", "chr2" ) , c(5,5)), transformation = "log2OddsRatio",
    chrom.level.lib = TRUE, lib.size.A = cbind(c("chr1", "chr2"), c(100, 12000)),
    lib.size.B = cbind(c("chr1", "chr2"), c(10000, 200)))
    transformData(seq_len(10), 10:1, transformation = "log2Ratio")

[Package NADfinder version 1.14.0 Index]