smoothRatiosByChromosome {NADfinder} | R Documentation

## Backgound correction and signal smoothing per chromosome

### Description

Split the ratios by chromosome and do background correction and signal smoothing.

### Usage

    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,
      ...
    )

### Arguments

`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.

### Value

A SimpleList of RangedSummarizedExperiment with smoothed ratios.

### Author(s)

Jianhong Ou, Haibo Liu and Julie Zhu

### Examples

    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)

[Package NADfinder version 1.18.0 Index]