transformData: transform counts to log2 cpm ratios, log2 ratios or log2 odds...

In jianhong/NADfinder: Call wide peaks for sequencing data

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")

jianhong/NADfinder documentation built on Oct. 29, 2023, 11:08 a.m.