hg19.GoNLsnps: Dataframe with overlaps GoNL variants and 450K probes
In molepi/omicsPrint: Cross omic genetic fingerprinting

Description Usage Format Source Examples

Dataframe containing all SNPs and short INDELS from GoNLv5 that overlap with 450K probes. This release does not include X and Y chromosomes, so only information for autosomal probes is available. For each overlap there is an unique row. Consequently, some probes are duplicated (probes that overlap with multiple variants) and some variants are duplicated (some variants overlap with more than one probe).

1	data(hg19.GoNLsnps)

A data frame with 207866 rows and 19 variables:

CHROM: chromosome, X and Y chromosomes are not available, since they are not included in this GoNL release
probe: probe ID
type: Infinium probedesign
strand: orientation of the probe
probeType: whether the probe measures a CpG-site (cg) or a non-CpG site (ch)
location_c: Location of the queried 'C' of the CpG dinucleotide. Note that this is the location of the C that is actually measured. For probes that interrogate the reverse strand (plus-strand probes) this is one base downstream of the C nucleotide on the forward strand
location_g: Location of the G nucleotide of the CpG dinucleotide. Note that this is the location of the queried G. For probes that interrogate the reverse strand (plus-strand probes) this is one base upstream of the G nucleotide on the forward strand
ID: SNP ID
snpBeg: Start coordinate of the variant. Identical to snpEnd for SNPs.
snpEnd: End coordinate of the variant. Identical to snpBeg for SNPs
AF: Allele frequency of alternative allele
REF: Reference allele
ALT: Alternative allele
FILTER: Filter information from GoNL.
MAF: Minor allele frequency
variantType: SNP or INDEL
distance_3end: Distance between SNP and 3'end of the probe. For type I probes the 3'end of the probe coincides with the queried C nucleotide. For type II probes the 3'end of the probe coincides with the G nucleotide directly after the C nucleotide.
distance_c: Distance from queried C nucleotide. A distance of -1 indicates that the SNPs overlaps the SBE-position for type I probes.
channel_switch: Indicates whether a variant in the SBE-location of type I probes causes a color-channel-switch or overlap with an INDEL. For plus-strand probes C/T, C/A and C/G SNPs are expected to cause a color-channel switch. For min-strand probes A/G, G/T and C/G SNPs are expected to cause a color-channel switch.

http://zwdzwd.github.io/InfiniumAnnotation

https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/

    data(hg19.GoNLsnps)
    
    # Select variants that overlap with queried C nucleotide
    snps_c <- hg19.GoNLsnps[hg19.GoNLsnps$distance_c == 0, ] 
    
    # Select all INDELS
    indels <- hg19.GoNLsnps[hg19.GoNLsnps$variantType == "INDEL",] 
    
    # Select SNPs that cause a channel-switch
    channel_switch <- hg19.GoNLsnps[!is.na(hg19.GoNLsnps$channel_switch)
& hg19.GoNLsnps$channel_switch == "Yes",]