[[,ChipInfo,ANY,ANY-method
Subset ChipInfo by chromosome
Retrieve the cytoband(s) for snp ids, genes or locations
Constructor (wrapper) for ChipInfo annotation object
Class to represent SNP annotation for a microarray
rownames method for GRanges objects
rownames method for ChipInfo objects
Retrieve the cytoband(s) for genes labels
Find the chromosome, start and end position for cytoband names
Extract chromosome numbers from GRanges/RangedData
Find the cytoband(s) overlapping a chromosome location
Select chromosome subset for ranged objects
Access alleles for ChipInfo
Convert from build 36 to build 37 SNP coordinates
Convert from build 37 to build 36 SNP coordinates
Find the chromosome, start and end position for gene names
Get human gene names and locations from biomart
Obtain subset of ranged object overlapping human genes
Convert gene ids to ensembl ids
Retrieve current ChipInfo annotation object
Find chromosome for SNP ids, gene name or band
Convert a chr:pos1-pos2 vector to a matrix
Convert a data.frame with positional information to GRanges
Convert ensembl ids to HGNC gene ids
Expand genomic locations to the ranges covering the 'n' closest SNPs
Find the chromosome position for SNP ids, gene name or band
extraColumnSlotNames2,ANY-method
Get extra column slot names
Find the gene(s) overlapping a chromosome location
Obtain a listing of known T1D associated genomic regions
ImmunoChip annotation object (built-in)
Obtain subset of ranged object overlapping known T1D associated genomic regions
Retrieve the Chip name for ChipInfo
Derive Telomere locations across the genome
Internal humarray Functions
chrInfo,RangedData-method
Chromosome info method for ranged objects
Convert from chip ID labels to dbSNP rs-ids
chrNames,RangedData-method
Chromosome names method for ranged objects
Order rs-ids or ichip ids by chrosome and position
Convert from build 37 to build 38 SNP coordinates
Return Centromere locations across the genome
Get chromosome lengths from build database
Convert from build 38 to build 37 SNP coordinates
Obtain nearby SNP-lists within a recombination window
Get HapMap recombination rates for hg18 (build 36)
Plot method for GRanges objects
Retrieve the 'n' closest GENE labels or positions near specified locus
Plot genes to annotate figures with genomic axes
Retrieve the UCSC build for a ChipInfo object
Retrieve the 'n' closest SNP ids or positions near specified locus
Plot the locations specified in a GRanges or RangedData object
As("ChipInfo", "GRanges")
Find closest SNPs to the starts and ends of ranges
Select chromosome subset of GRanges or RangedData object
Force a valid genomic range, given the inputted coordinates
Chromosome method for RangedData objects
Retreive GO terms from biomart for a given gene list
Make a compact version of gene annotation
Simplify Analysis and Annotation of Human Microarray Datasets
Autoimmune enriched regions as mapped on ImmunoChip
Convert ChipInfo between build 36/37/38 coordinates
Normalize Lambda inflation factors to specific case-control count
Access quality control pass or fail codes for ChipInfo
Wrapper to construct GRanges object from chr,pos or chr,start,end
Access chip-ids for ChipInfo
Select all ranges lying within a chromosome window
chrIndices,RangedData-method
Chromosome indices method for ranged objects
Invert a ranged object
Select the empty space between ranges for the whole genome, for instance you may want
to overlap with everything NOT in a set of ranges.
Access rs-ids for ChipInfo
Convert a data.frame with positional information to RangedData/GRanges
Convert RangedData/GRanges to a data.frame
Convert from dbSNP rs-ids to chip ID labels
Convert GRanges/RangedData to chr:pos1-pos2 vector
Select ranges only within the 22 autosomes in a ranged data object
Retrieve SNP ids or positions in specified range
Change the chromosome labels in a RangedData or GRanges object to string codes
Find closest SNPs to the ends of ranges
Download GWAS hits from t1dbase.org
Return Cytoband/Karyotype locations across the genome
Retrieve locations of Immunoglobin regions across the genome
Get exon names and locations from UCSC
Find closest SNPs to the starts of ranges
Convert from chip/rs-ids to manifest chip ID labels
Simulate a GRanges or RangedData object
Meta-analysis using odds ratio and standard error from 2 datasets
Change the chromosome labels in a RangedData or GRanges object to numbers
Extend an interval or SNP by distance in centimorgans (recombination distance)
Display a ChipInfo object
Returns the A and B allele for SNP ids