A1                      Access alleles for ChipInfo
AB                      Returns the A and B allele for SNP ids
Band                    Retrieve the cytoband(s) for snp ids, genes or
                        locations
Band.gene               Retrieve the cytoband(s) for genes labels
Band.pos                Find the cytoband(s) overlapping a chromosome
                        location
ChipInfo                Constructor (wrapper) for ChipInfo annotation
                        object
ChipInfo-class          Class to represent SNP annotation for a
                        microarray
Chr                     Find chromosome for SNP ids, gene name or band
ENS.to.GENE             Convert ensembl ids to HGNC gene ids
GENE.to.ENS             Convert gene ids to ensembl ids
Gene.pos                Find the gene(s) overlapping a chromosome
                        location
ImmunoChipB37           ImmunoChip annotation object (built-in)
Pos                     Find the chromosome position for SNP ids, gene
                        name or band
Pos.band                Find the chromosome, start and end position for
                        cytoband names
Pos.gene                Find the chromosome, start and end position for
                        gene names
QCcode                  Access quality control pass or fail codes for
                        ChipInfo
[[,ChipInfo,ANY,ANY-method
                        Subset ChipInfo by chromosome
as                      As("ChipInfo", "GRanges")
chip                    Retrieve the Chip name for ChipInfo
chip.support            Retrieve current ChipInfo annotation object
chipId                  Access chip-ids for ChipInfo
chrIndices-methods      ~~ Methods for Function 'chrIndices' ~~
chrInfo-methods         ~~ Methods for Function 'chrInfo' ~~
chrNames-methods        ~~ Methods for Function 'chrNames' ~~
chrNums                 Extract chromosome numbers from
                        GRanges/RangedData
chrSel                  Select chromosome subset for ranged objects
chrSelect               Select chromosome subset of GRanges or
                        RangedData object
chrm                    Chromosome method for RangedData objects
coerce-methods          ~~ Methods for Function 'coerce' ~~
coerce<--methods        ~~ Methods for Function 'coerce<-' ~~
compact.gene.list       Make a compact version of gene annotation
conv.36.37              Convert from build 36 to build 37 SNP
                        coordinates
conv.37.36              Convert from build 37 to build 36 SNP
                        coordinates
conv.37.38              Convert from build 37 to build 38 SNP
                        coordinates
conv.38.37              Convert from build 38 to build 37 SNP
                        coordinates
convTo37                Convert ChipInfo between build 36/37/38
                        coordinates
convert.textpos.to.data
                        Convert a chr:pos1-pos2 vector to a matrix
df.to.GRanges           Convert a data.frame with positional
                        information to GRanges
df.to.ranged            Convert a data.frame with positional
                        information to RangedData/GRanges
endSnp                  Find closest SNPs to the ends of ranges
expand.nsnp             Expand genomic locations to the ranges covering
                        the 'n' closest SNPs
extraColumnSlotNames2-methods
                        ~~ Methods for Function 'extraColumnSlotNames2'
                        ~~
force.chr.pos           Force a valid genomic range, given the inputted
                        coordinates
get.GO.for.genes        Retreive GO terms from biomart for a given gene
                        list
get.centromere.locs     Return Centromere locations across the genome
get.chr.lens            Get chromosome lengths from build database
get.cyto                Return Cytoband/Karyotype locations across the
                        genome
get.exon.annot          Get exon names and locations from UCSC
get.gene.annot          Get human gene names and locations from biomart
get.genic.subset        Obtain subset of ranged object overlapping
                        human genes
get.immunobase.snps     Download GWAS hits from t1dbase.org
get.immunog.locs        Retrieve locations of Immunoglobin regions
                        across the genome
get.nearby.snp.lists    Obtain nearby SNP-lists within a recombination
                        window
get.recombination.map   Get HapMap recombination rates for hg18 (build
                        36)
get.t1d.regions         Obtain a listing of known T1D associated
                        genomic regions
get.t1d.subset          Obtain subset of ranged object overlapping
                        known T1D associated genomic regions
get.telomere.locs       Derive Telomere locations across the genome
humarray-package        Simplify Analysis and Annotation of Human
                        Microarray Datasets
iChipRegionsB36         Autoimmune enriched regions as mapped on
                        ImmunoChip
id.to.rs                Convert from chip ID labels to dbSNP rs-ids
ids.by.pos              Order rs-ids or ichip ids by chrosome and
                        position
in.window               Select all ranges lying within a chromosome
                        window
invGRanges              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.
lambda_1000             Normalize Lambda inflation factors to specific
                        case-control count
makeGRanges             Wrapper to construct GRanges object from
                        chr,pos or chr,start,end
manifest                Convert from chip/rs-ids to manifest chip ID
                        labels
meta.me                 Meta-analysis using odds ratio and standard
                        error from 2 datasets
nearest.gene            Retrieve the 'n' closest GENE labels or
                        positions near specified locus
nearest.snp             Retrieve the 'n' closest SNP ids or positions
                        near specified locus
plot,GRanges,ANY-method
                        Plot method for GRanges objects
plotGeneAnnot           Plot genes to annotate figures with genomic
                        axes
plotRanges              Plot the locations specified in a GRanges or
                        RangedData object
rangeSnp                Find closest SNPs to the starts and ends of
                        ranges
ranged.to.data.frame    Convert RangedData/GRanges to a data.frame
ranged.to.txt           Convert GRanges/RangedData to chr:pos1-pos2
                        vector
recomWindow             Extend an interval or SNP by distance in
                        centimorgans (recombination distance)
rownames,ChipInfo-method
                        rownames method for ChipInfo objects
rownames,GRanges-method
                        rownames method for GRanges objects
rownames<--methods      ~~ Methods for Function 'rownames<-' ~~
rranges                 Simulate a GRanges or RangedData object
rs.id                   Access rs-ids for ChipInfo
rs.to.id                Convert from dbSNP rs-ids to chip ID labels
select.autosomes        Select ranges only within the 22 autosomes in a
                        ranged data object
set.chr.to.char         Change the chromosome labels in a RangedData or
                        GRanges object to string codes
set.chr.to.numeric      Change the chromosome labels in a RangedData or
                        GRanges object to numbers
showChipInfo            Display a ChipInfo object
snps.in.range           Retrieve SNP ids or positions in specified
                        range
startSnp                Find closest SNPs to the starts of ranges
ucsc                    Retrieve the UCSC build for a ChipInfo object
