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

Description Usage Arguments Value Author(s) Examples

View source: R/transformData.R

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

1
2
3
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
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")

LihuaJulieZhu/NADfinder documentation built on May 17, 2019, 6:21 p.m.