Package index

All functions

methylation_score()

Various methylation scores

correct_dye_bias() correct_dye_bias2() dont_normalize()

Functions for preprocessing

call_genotypes() mxm_() snp_outliers() eBeta()

Genotype calling

estimateLC()

Cell composition

check_sex() predict_sex()

Infer the sex of sample donor

check_snp_agreement() agreement_() enumerate_sample_donors()

Agreement of SNPs

control_metrics() sample_failure()

Quality control metrics

summits() detectionP() detectionP.neg() mask() eval_detP_cutoffs() detectionP.minfi()

Detection p-values

drop_samples()

Drop samples from raw data.

read_idats()

Read .idat files