methylation_specificity: compute methylation specificity for spike-in standards

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

compute methylation specificity for spike-in standards

Description

In a cfMeDIP experiment, the yield of methylated fragments should be >95% (ideally 98-99%) due to the nature of the assay.

Usage

methylation_specificity(spike_gr, spike)

Arguments

spike_gr	GRanges of spike contigs (e.g. output object from scan_spiked_bam, scan_spike_contigs, or scan_spike_bedpe)
spike	spike contig database, if needed (e.g. data(spike))

Value

         list with median and mean coverage across spike contigs

Examples

data(genomic_res)
data(spike_res)
data(spike, package="spiky")
methylation_specificity(spike_res, spike=spike)

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