crossarrayEWAS

Design-aware region and block detection for longitudinal EWAS that combines Illumina 450K and EPIC samples. This is the numerical core of the ewas-crossarray-harmonise pipeline, packaged so the Galaxy wrappers and the Nextflow stages can depend on a version rather than vendoring the script.

Installation

Once accepted into Bioconductor:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("crossarrayEWAS")

Development version:

BiocManager::install("kkamieniecka/ewas-crossarray-harmonise",
                     subdir = "pkg/crossarrayEWAS")

Scope

fit_within() estimates the exposure effect within subject for every probe, absorbing subject, array type and chip. comethylation_clusters() groups adjacent probes that co-vary within subject. distance_penalty() and tv_denoise() produce a piecewise-constant effect track whose jumps are the region boundaries, which call_regions() reports with a precision-weighted effect and standard error. fit_block_hsmm() and call_blocks() call long-range blocks from a distance-aware three-state hidden semi-Markov model. stability_selection() and within_subject_permutation() resample subjects, not samples.

Status: pre-submission skeleton. See NEWS.md for what is still missing.