classification_CpG_SNP_450K: Classification of CpG/SBE-SNPs in the Illumina Infinium...

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

Classification of CpG/SBE-SNPs in the Illumina Infinium HumanMethylation450 Beadchip microarray

Description

Includes a list containing processed vcf files in 16 categories:

• II_plus_SNP1_C_TA: Infinium type-II probe, targeting (+)-strand, SNP at position 1, Alleles: C ⇔ A/T

• II_plus_SNP1_C_G: Infinium type-II probe, targeting (+)-strand, SNP at position 1, Alleles: C ⇔ G

• II_plus_SNP2_G_ACT: Infinium type-II probe, targeting (+)-strand, SNP at position 2, Alleles: G ⇔ A/C/T

• II_minus_SNP1_C_AGT: Infinium type-II probe, targeting (-)-strand, SNP at position 1, Alleles: C ⇔ A/G/T

• II_minus_SNP2_G_TA: Infinium type-II probe, targeting (-)-strand, SNP at position 2, Alleles: G ⇔ A/T

• II_minus_SNP2_G_C: Infinium type-II probe, targeting (-)-strand, SNP at position 2, Alleles: G ⇔ C

• I_plus_SNP0_A_C_T: Infinium type-I probe, targeting (+)-strand, SNP at position 0, Alleles: A ⇔ C ⇔ T

• I_plus_SNP0_ACT_G: Infinium type-I probe, targeting (+)-strand, SNP at position 0, Alleles: A/C/T ⇔ G

• I_plus_SNP1_C_T: Infinium type-I probe, targeting (+)-strand, SNP at position 1, Alleles: C ⇔ T

• I_plus_SNP1_C_AG: Infinium type-I probe, targeting (+)-strand, SNP at position 1, Alleles: C ⇔ A/G

• I_plus_SNP2_G_ACT: Infinium type-I probe, targeting (+)-strand, SNP at position 2, Alleles: G ⇔ A/C/T

• I_minus_SNP1_C_AGT: Infinium type-I probe, targeting (-)-strand, SNP at position 1, Alleles: A ⇔ A/G/T

• I_minus_SNP2_G_A: Infinium type-I probe, targeting (-)-strand, SNP at position 2, Alleles: G ⇔ A

• I_minus_SNP2_G_CT: Infinium type-I probe, targeting (-)-strand, SNP at position 2, Alleles: G ⇔ C/T

• I_minus_SNP3_A_G_T: Infinium type-I probe, targeting (-)-strand, SNP at position 3, Alleles: A ⇔ G ⇔ T

• I_minus_SNP3_AGT_C: Infinium type-I probe, targeting (-)-strand, SNP at position 3, Alleles: A/G/T ⇔ C

Categories are mutually exclusive. Triallelic SNPs have been excluded at this point. For more information concerning the logic of this classification, please check the associated paper (see References). 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(classification_CpG_SNP_450K)

Format

An object of class list

References

Revisiting Genetic artefacts on DNA methylation microarrays. Genome Research

Examples

data(classification_CpG_SNP_450K)

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