shrinkBins {compartmap} | R Documentation

## Employ an eBayes shrinkage approach for bin-level estimates for A/B inference

### Description

`shrinkBins` returns shrunken bin-level estimates

### Usage

    shrinkBins(
      x,
      original.x,
      prior.means = NULL,
      chr = NULL,
      res = 1e+06,
      targets = NULL,
      jse = TRUE,
      assay = c("rna", "atac"),
      genome = c("hg19", "hg38", "mm9", "mm10")
    )

### Arguments

`x` | Input SummarizedExperiment object
`original.x` | Full sample set SummarizedExperiment object
`prior.means` | The means of the bin-level prior distribution
`chr` | The chromosome to operate on
`res` | Resolution to perform the binning
`targets` | The column/sample/cell names to shrink towards
`jse` | Whether to use a James-Stein estimator (default is TRUE)
`assay` | What assay type this is ("rna", "atac")
`genome` | What genome are we working with ("hg19", "hg38", "mm9", "mm10")

### Details

This function computes shrunken bin-level estimates using a James-Stein estimator, reformulated as an eBayes procedure

### Value

A list object to pass to getCorMatrix

### Examples

    data("k562_scrna_chr14", package = "compartmap")
    shrunken.bin.scrna <- shrinkBins(x = k562_scrna_chr14,
                                     original.x = k562_scrna_chr14,
                                     chr = "chr14", assay = "rna")

[Package compartmap version 1.10.0 Index]