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