Call LOI samples over al imprinted loci.

LOI_calling calls LOI samples based on binomial p-value.

LOI_calling(data_hash, samples_all, SE)

Arguments

data_hash

Hash. Hash of SNP positions with a data frame for every position with at least columns of allelic counts ("A", "T", "C", "G"), reference and variants counts ("ref_count" and "var_count", respectively) and sample ids ("samples").

samples_all

Character list. List of all sample names.

SE

Number. Sequencing error rate.

Value

Data frame with LOI calls per samples. The data frame contains sample ids ("samples"), number of least and most expressed alleles ("least" and "most", respectively), a quality check ("warning"), binomial p-values ("binom"), FDR adjusted p-values ("FDR") and LOI vs not LOI calls ("geno"). A "!" in the warning column indicates that more non-standard alleles than standard alleles were present for a sample (with a count of at least 2).