hg19.GoNLsnps {omicsPrint} | R Documentation

## Dataframe with overlaps GoNL variants and 450K probes

### Description

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).

### Usage

    data(hg19.GoNLsnps)

### Format

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.

### Source

http://zwdzwd.github.io/InfiniumAnnotation

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

### Examples

        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",]

[Package omicsPrint version 1.10.0 Index]