scan_methylation_specificity: tabulate methylation specificity for multiple spike-in...

In trichelab/spiky: Spike-in calibration for cell-free MeDIP

tabulate methylation specificity for multiple spike-in BAM/CRAM files

Description

Methylation specificity is here defined as methylated_spike_covg/spike_covg

Usage

scan_methylation_specificity(files, spike, sep = "_")

Arguments

files	a vector of BAM/CRAM file names
spike	a spike-in database
sep	the separator for spike-in contig names ("_")

Value

   a matrix with columns "mean" and "median"

Examples

data(spike) 
library(GenomicRanges)
sb <- system.file("extdata", "example.spike.bam", package="spiky", 
                  mustWork=TRUE)
scan_methylation_specificity(sb, spike=spike)

trichelab/spiky documentation built on Sept. 17, 2022, 8:44 a.m.