calc_derivedasm {DAMEfinder} | R Documentation

## Calculate SNP-based ASM

### Description

Combines all the `GRangeslist` generated in `extract_bams` into a `RangedSummarizedExperiment` object, and calculates SNP-based allele-specific methylation.

### Usage

    calc_derivedasm(sampleList, cores = 1, verbose = TRUE)

### Arguments

`sampleList` | List of samples returned from `extract_bams`.
`cores` | Number of cores to thread.
`verbose` | If the function should be verbose.

### Value

`RangedSummarizedExperiment` containing in assays:

- der.ASM: matrix with SNP-based ASM

- snp.table: Matrix with SNP associated to the CpG site.

- ref.cov: Coverage of the 'reference' allele.

- alt.cov: Coevarage of the 'alternative' allele.

- ref.meth: Methylated reads from the 'reference' allele.

- alt.meth: Methylated reads from the 'alternative' allele.

### Examples

    data(extractbams_output)
    derASM <- calc_derivedasm(extractbams_output[c(1,2)], cores = 1,
       verbose = FALSE)

[Package DAMEfinder version 1.6.0 Index]