calc_derivedasm: Calculate SNP-based ASM

In DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

Description

Combines all the GRangeslist generated in extract_bams into a RangedSummarizedExperiment object, and calculates SNP-based allele-specific methylation. TODO: Doesn't work for one sample

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)

DAMEfinder documentation built on Nov. 8, 2020, 11:10 p.m.