log2se {NADfinder} | R Documentation |
Calculate the log2 transformed ratios for nucleolus vs genome. pseudo-count will be used to avoid x/0 or log(0).
log2se(se, nucleolusCols, genomeCols, pseudocount = 1L, transformation = c("log2OddsRatio", "log2CPMRatio", "log2Ratio"), chrom.level.lib = TRUE)
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 |
A RangedSummarizedExperiment object with log2 transformed ratios. Assays will be named as nucleolus, genome and ratio.
Jianhong Ou and Julie Zhu
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") as.data.frame(assays(log2se(se, nucleolusCols = c("A", "C"), genomeCols = c("B", "D"), transformation = "log2Ratio"))) as.data.frame(assays(log2se(se, nucleolusCols = c("A", "C"), genomeCols = c("B", "D"), transformation = "log2CPMRatio"))) as.data.frame(assays(log2se(se, nucleolusCols = c("A", "C"), genomeCols = c("B", "D"), transformation = "log2OddsRatio")))