Make CAMDAC methylation panel from allele counts Methylation fractions are obtained by summing M and UM reads across samples

Make CAMDAC methylation panel from allele counts Methylation fractions are obtained by summing M and UM reads across samples

panel_meth_from_counts(
  ac_files,
  ac_props = NULL,
  min_coverage = 3,
  min_samples = 1,
  max_sd = 1,
  drop_snps = FALSE,
  cores = 5
)

Arguments

ac_files

Allele count files from CAMDAC

ac_props

Proportions of each sample to use in panel. If NULL, samples are weighted by their total number of reads, which equals the sum of M and UM counts. If samples are NA, then proportions are redistributed.

min_coverage

Minimum coverage for a sample's site to be included in panel

min_samples

Minimum number of samples with coverage for a site to be included in panel

max_sd

Maximum standard deviation of methylation for a site to be included in panel

drop_snps

Boolean. If TRUE, drop per-sample CG-SNPs (BAF < 0.1 or BAF > 0.9) from panel

cores

Number of cores to use for calculating HDI