Design-Aware Region and Block Detection for Cross-Array Longitudinal EWAS

Documentation for package ‘crossarrayEWAS’ version 0.99.1

as_granges	Region or block calls as a GRanges
call_blocks	Call blocks from the state posterior
call_regions	Turn a denoised effect track into regions
comethylation_clusters	Group adjacent probes that co-vary within subject
distance_penalty	Distance-decaying penalty for the denoising step
ewas_blocks	Call long-range methylation blocks from a methylation object
ewas_regions	Call differentially methylated regions from a methylation object
fit_block_hsmm	Distance-aware three-state hidden semi-Markov block model
fit_within	Within-subject (fixed-effects) probe-level fit
fit_within_se	Fit the within-subject exposure effect on a SummarizedExperiment
moderate_variance	Empirical-Bayes shrinkage of per-probe residual variance
naive_permutation	Permute the exposure across all samples
probe_coords	Probe chromosome and position from an annotated object
read_f64	Read a raw float64 matrix written by the pipeline
sort_probes	Order an object by probe position
stability_selection	Subject-level stability selection
tv_denoise	Total-variation denoising of a probe-level effect track
within_subject_permutation	Permute the exposure within subject