shrinkBins {compartmap} | R Documentation |
shrinkBins
returns shrunken bin-level estimates
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") )
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") |
This function computes shrunken bin-level estimates using a James-Stein estimator, reformulated as an eBayes procedure
A list object to pass to getCorMatrix
data("k562_scrna_chr14", package = "compartmap") shrunken.bin.scrna <- shrinkBins(x = k562_scrna_chr14, original.x = k562_scrna_chr14, chr = "chr14", assay = "rna")