getCorrelations {NADfinder} | R Documentation

## Get correlation coefficinets and p-values between biological replicates

### Description

Get correlations and p-values between biological replicates based on coverage signal for peak regions. The signals will be filtered by the background cutoff value before calculated correlations. This function also output a correlation plots using the corrplot.

### Usage

    getCorrelations(
      se,
      chr = paste0("chr", seq_len(19)),
      ratioAssay = "ratio",
      window = 10000L,
      cutoff = 1,
      method = c("spearman", "pearson", "kendall"),
      file_name = "Correlation plots.pdf",
      ...
    )

### Arguments

`se` | A RangedSummarizedExperiment object. The output from log2se.
`chr` | A vector of character. Filter for seqnames. It should be the chromosome names to be kept.
`ratioAssay` | character(1). Column name of ratio for correlation calculation.
`window` | numeric(1) or integer(1). The window size for summary of the ratios.
`cutoff` | numeric(1). All the coverage signals lower than cutoff value in a given window will be filtered out.
`method` | character(1) indicating which correlation coefficient is to be computed. See cor.
`file_name` | A file name for output correlation plots
`...` | Parameters not used.

### Value

A list of matrixes of correlation coefficients and p-values.

### Author(s)

Jianhong Ou, Haibo Liu

### Examples

    data(triplicate.count)
    se <- triplicate.count
    se <- log2se(se, transformation = "log2CPMRatio",
                 nucleolusCols = c("N18.subsampled.srt-2.bam",
                 "N18.subsampled.srt-3.bam",
                 "N18.subsampled.srt.bam"),
                 genomeCols = c("G18.subsampled.srt-2.bam",
                 "G18.subsampled.srt-3.bam",
                 "G18.subsampled.srt.bam"))
    getCorrelations(se, chr="chr18")

[Package NADfinder version 1.14.0 Index]