EPICv2manifest is an annotation package providing a data.frame object containing the complete 49 column Infinium Illumina EPIC v2.0 probe manifest (“IlmnID” constitutes the rownames), plus 31 additional columns derived from Peters et al. (2024):
CpG_chrm, CpG_beg, CpG_end - EPICv2 coordinates from Sesame manifest
MismatchPos - vector of probes where “Y” indicates discrepant genomic position between Sesame and Illumina, includes those that are missing mapping information in Illumina manifest (chr0)
MissingPos - vector of probes where “Y” indicates probes missing mapping information in Illumina manifest
namerep - vector of probes where “Y” indicates probes that have replicates based on probe name match (this vector can be married up with Name column to select a single probe to represent each name replicate)
seqrep - vector of probes where “Y” indicates probes that have exact sequence matches with other probes within EPICv2
seqrep_IlmnIDs - IlmnIDs of those probes with exact sequence matches with other probes within EPICv2 (corresponding to seqrep)
seqrep_RepNum - replicate number of those probes with exact sequence matches with other probes within EPICv2 (corresponding to seqrep and seqrep_IlmnIDs). Can be used to e.g. filter for only 1 probe per sequence-replicate.
posrep - vector of probes where “Y” indicates probes that have exact genomic position matches with other probes within EPICv2 (based on Illumina genomic positions – note, none of the affected probes are discrepant with Sesame mapping)
posrep_IlmnIDs - IlmnIDs of those probes with exact genomic position matches with other probes within EPICv2 (corresponding to posrep)
posrep_RepNum - replicate number of those probes with exact genomic position matches with other probes within EPICv2 (corresponding to posrep and posrep_IlmnIDs). Can be used to e.g. filter for only 1 probe per genomic-position-replicate.
EPICv1probeID - vector of EPICv1 probe names where probe names match between EPICv1 and EPICv2
EPICv1seqmatch - vector of EPICv1 probe names where probe sequences match between EPICv1 and EPICv2
EPICv1locmatch - vector of EPICv1 probe names where genomic locations match between EPICv1 and EPICv2 (based on Sesame locations)
K450probeID - vector of 450K probe names where probe names match between 450K and EPICv2
K450seqmatch - vector of 450K probe names where probe sequences match between 450K and EPICv2
K450locmatch - vector of 450K probe names where genomic locations match between 450K and EPICv2 (based on Sesame locations)
K450locmatch2 - vector of 450K probe names where additional 450K probes have a genomic location match between 450K and EPICv2 (based on Sesame locations)
K27probeID - vector of 27K probe names where probe names match between 27K and EPICv2
K27seqmatch - vector of 27K probe names where probe sequences match between 27K and EPICv2
K27locmatch - vector of 27K probe names where genomic locations match between 27K and EPICv2 (based on Sesame locations)
K27locmatch2 - vector of 27K probe names where additional 27K probes have a genomic location match between 27K and EPICv2 (based on Sesame locations)
CH_BLAT - vector of probes where “Y” indicates at least one in silico cross-hybridisation event (\(\ge 47\) bp match) to a non-target region of the genome, predicted by BLAT (Kent 2002)
CH_WGBS_evidence – subset vector of CH_BLAT where “Y” indicates a greater affinity for the off-target(s), via comparison to whole genome bisulphite sequencing on matched samples
RMSE_with_WGBS – root mean squared error when comparing probe methylation to matched target CpG site methylation from WGBS M-values)
Num_offtargets – number of off-target in silico hybridisation events predicted by the probe sequence via BLAT (Kent 2002)
Suggested_offtarget - if CH_WGBS_evidence == "Y", the hg38 coordinate of the off-target cytosine conferring minimum RMSE with WGBS
Rep_results_by_NAME – results of competitive comparison between replicates, with replicate probe sets defined by column Name
Rep_results_by_SEQUENCE - results of competitive comparison between replicates, with replicate probe sets defined by column seqrep_IlmnIDs
Rep_results_by_LOCATION - results of competitive comparison between replicates, with replicate probe sets defined by column posrep_IlmnIDs
To access the EPICv2manifest object, please run the following:
library(AnnotationHub)
ah <- AnnotationHub()
EPICv2manifest <- ah[["AH116484"]]sessionInfo()Peters, T.J., Meyer, B., Ryan, L. et al. (2024). Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 25, 251. https://doi.org/10.1186/s12864-024-10027-5
Kent, W. J. (2002). BLAT–the BLAST-like alignment tool. Genome Research, 12(4), 656–664.