smoothRatiosByChromosome {NADfinder} | R Documentation |
Split the ratios by chromosome and do background correction and signal smoothing.
smoothRatiosByChromosome( se, chr = paste0("chr", c(seq_len(21), "X", "Y")), ratioAssay = "ratio", backgroundCorrectedAssay = "bcRatio", smoothedRatioAssay = "smoothedRatio", zscoreAssay = "zscore", backgroundPercentage = 0.25, chrom.level.background = TRUE, ... )
se |
An object of RangedSummarizedExperiment with log2-transformed ratios, CPMRatios or OddRatios. Output of log2se |
chr |
A character vector, used to filter out seqnames. It should be the chromosome names to be kept. |
ratioAssay |
The name of assay in se, which store the values (log2-transformed ratios, CPMRatios or OddRatios) to be smoothed. |
backgroundCorrectedAssay, smoothedRatioAssay, zscoreAssay |
character(1). Assays names for background corrected ratios, smoothed ratios and z-scores based on background corrected ratios. |
backgroundPercentage |
numeric(1). Percentage of values for background, see zscoreOverBck. The percentage of values lower than this threshold will be treated as background, with 25 percentile as default. |
chrom.level.background |
logical(1): TRUE or FALSE, default to TRUE, use chromosome-level background to calculate z-score |
... |
Parameters could be passed to butterFilter. |
A SimpleList of RangedSummarizedExperiment with smoothed ratios.
Jianhong Ou, Haibo Liu and Julie Zhu
data(single.count) se <- single.count dat <- log2se(se, nucleolusCols="N18.subsampled.srt.bam", genomeCols="G18.subsampled.srt.bam", transformation="log2CPMRatio") dat1 <- smoothRatiosByChromosome(dat, N=100, chr = c("chr18", "chr19")) dat2 <- smoothRatiosByChromosome(dat, N=100, chr = c("chr18", "chr19"), chrom.level.background = FALSE)