annot_450K: Genetic variants associated to Illumina Infinium...

In BenjaminPlanterose/UMtools: An R-package for analysing Illumina DNA Methylation arrays at the fluorescence intensity level

Genetic variants associated to Illumina Infinium HumanMethylation450 Beadchip probes

Description

Includes a list containing processed vcf files in 6 categories:

• CpG_SNP

• SBE_SNP

• probe_SNP

• CpG_indel

• SBE_indel

• probe_indel

These files were obtained by intersecting 450K probe coordinates with common variants in dbSNP151 file 00-common_all.vcf. Additionally, we segregated SNPs from indels and kept only variants with MAF > 0.01. All scripts employed can be found at UMtools/scripts/.

Column names correspond to the following:

• SNP_chr: SNP chromosome number

• SNP_pos: SNP position (hg19/GRCh37)

• rs: SNP identifier in dbSNP

• REF: Reference allele

• ALT: Alternate allele

• QUAL: Quality (not available on dbSNP, hence, simply .)

• FILTER: Filter (not available on dbSNP, hence, simply .)

• INFO: Contains metadata of the variant; for more information, consult .vcf formating rules (https://www.ncbi.nlm.nih.gov/snp/docs/products/vcf/redesign/). Here, in summary, we highlight: GENEINFO (closest gene to the SNP), CAF (Common Allele frequency) and VC (variant class: either SNV (single-nucleotide variant) or DIV (deletion and insertion variants))

• CpG_chr: CpG chromosome number

• CpG_start: probe region start (hg19/GRCh37), input into bedtools (consider that bedtools employed intervals from the form (a,b]

• CpG_end: probe region end (hg19/GRCh37), input into bedtools (consider that bedtools employed intervals from the form (a,b]

• cg: CpG identifier (see IlluminaHumanMethylation450kanno.ilmn12.hg19)

Usage

data(annot_450K)

Format

An object of class list

References

Revisiting Genetic artefacts on DNA methylation microarrays. Genome Research

Examples

data(annot_450K)

BenjaminPlanterose/UMtools documentation built on Aug. 19, 2024, 4:54 a.m.