LDSearch(SNPs, dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.8,
distanceLimit = 500, GeneCruiser = TRUE, quiet = FALSE)rel21:rel22:hapmap3r2:onekgpilot:Proxy:The proxy SNP matched to the queried
SNP.SNP: The SNP queried.Distance: The distance, in base pairs, between
the queried SNP and the proxy SNP. This distance is
calculated according to up-to-date position information
returned from NCBI.RSquared: The measure of
LD between the SNP and the proxy.DPrime:
Another measure of LD between the SNP and the proxy.GeneVariant: Present if GeneCruiser is
TRUE. This will identify where the SNP lies relative
to its 'parent' SNP.GeneName: Present if
GeneCruiser is TRUE. If the proxy SNP found
lies within a gene, the name of that gene will be returned
here. Otherwise, the field is N/A.GeneDescription: Present if GeneCruiser
is TRUE. If the proxy SNP lies within a gene,
information about that gene (as obtained from GeneCruiser)
will be available here.Major: The major
allele, as reported by SNAP. Minor: The minor
allele, as reported by SNAP. MAF: The minor
allele frequency corresponding to the reference panel
queried, as obtained through SNAP.NObserved:
The number of individuals from which the MAF information is
generated, for column MAF.Chromosome_NCBI: The chromosome that the marker lies
on. Marker_NCBI: The name of the marker. If
the rs ID queried has been merged, the up-to-date name of
the marker is returned here, and a warning is issued. Class_NCBI: The marker's 'class'. See
Gene_NCBI: If the marker
lies within a gene (either within the exon or introns of a
gene), the name of that gene is returned here; otherwise,
NA. Note that the gene may not be returned if the
marker lies too far upstream or downstream of the
particular gene of interest. Alleles_NCBI: The
alleles associated with the SNP if it is a SNV; otherwise,
if it is an INDEL, microsatellite, or other kind of
polymorphism the relevant information will be available
here. Major_NCBI: The major allele of the SNP,
on the forward strand, given it is an SNV; otherwise,
NA. Minor_NCBI: The minor allele of the
SNP, on the forward strand, given it is an SNV; otherwise,
NA. MAF_NCBI: The minor allele
frequency of the SNP, given it is an SNV. This is drawn
from the current global reference population used by NCBI.
BP_NCBI: The chromosomal position, in base
pairs, of the marker, as aligned with the current genome
used by dbSNP.Information on the HapMap populations:
Information on the 1000 Genomes populations:
YRIJPT+CHBCHDGIHLWKMEKMKKTSICEU+TSIJPT+CHB+CHDASWTRUE