Find the chromosome, start and end position for gene names
Convert a data.frame with positional information to RangedData/GRanges
Convert ChipInfo between build 36/37/38 coordinates
Change the chromosome labels in a RangedData or GRanges object to string codes
Obtain subset of ranged object overlapping human genes
Select all ranges lying within a chromosome window
~~ Methods for Function toGenomeOrder ~~
Retrieve SNP ids or positions in specified range
Find the cytoband(s) overlapping a chromosome location
Access chip-ids for ChipInfo
~~ Methods for Function chrInfo ~~
Convert from build 36 to build 37 SNP coordinates
Get exon names and locations from UCSC
Obtain nearby SNP-lists within a recombination window
Order rs-ids or ichip ids by chrosome and position
Plot method for GRanges objects
Access rs-ids for ChipInfo
Convert ensembl ids to HGNC gene ids
Convert gene ids to ensembl ids
Select chromosome subset for ranged objects
Make a compact version of gene annotation
Expand genomic locations to the ranges covering the 'n' closest SNPs
Retrieve the 'n' closest GENE labels or positions near specified locus
Wrapper to construct GRanges object from chr,pos or chr,start,end
Simulate a GRanges or RangedData object
Display a ChipInfo object
Retrieve the Chip name for ChipInfo
Convert a data.frame with positional information to GRanges
~~ Methods for Function rownames<- ~~
Get chromosome lengths from build database
Retrieve the UCSC build for a ChipInfo object
Find closest SNPs to the starts of ranges
Obtain subset of ranged object overlapping known T1D associated genomic regions
rownames method for ChipInfo objects
Class to represent SNP annotation for a microarray
Retrieve the cytoband(s) for genes labels
Find chromosome for SNP ids, gene name or band
Access quality control pass or fail codes for ChipInfo
Extract chromosome numbers from GRanges/RangedData
Convert from build 37 to build 36 SNP coordinates
Convert a chr:pos1-pos2 vector to a matrix
Internal humarray Functions
Convert from dbSNP rs-ids to chip ID labels
Convert RangedData/GRanges to a data.frame
Chromosome method for RangedData objects
Normalize Lambda inflation factors to specific case-control count
Plot genes to annotate figures with genomic axes
Change the chromosome labels in a RangedData or GRanges object to numbers
Return Cytoband/Karyotype locations across the genome
ImmunoChip annotation object (built-in)
~~ Methods for Function coerce<- ~~
Retrieve current ChipInfo annotation object
Download GWAS hits from t1dbase.org
Convert from chip ID labels to dbSNP rs-ids
Simplify Analysis and Annotation of Human Microarray Datasets
Extend an interval or SNP by distance in centimorgans (recombination distance)
Find the gene(s) overlapping a chromosome location
As("ChipInfo", "GRanges")
~~ Methods for Function chrNames ~~
~~ Methods for Function chrIndices ~~
Force a valid genomic range, given the inputted coordinates
Get HapMap recombination rates for hg18 (build 36)
Return Centromere locations across the genome
Select ranges only within the 22 autosomes in a ranged data object
Retrieve the 'n' closest SNP ids or positions near specified locus
Find closest SNPs to the starts and ends of ranges
Returns the A and B allele for SNP ids
[[,ChipInfo,ANY,ANY-method
Subset ChipInfo by chromosome
Retrieve locations of Immunoglobin regions across the genome
Derive Telomere locations across the genome
Select chromosome subset of GRanges or RangedData object
Plot the locations specified in a GRanges or RangedData object
Convert from chip/rs-ids to manifest chip ID labels
Convert GRanges/RangedData to chr:pos1-pos2 vector
rownames method for GRanges objects
Constructor (wrapper) for ChipInfo annotation object
Retrieve the cytoband(s) for snp ids, genes or locations
Find the chromosome, start and end position for cytoband names
Convert from build 37 to build 38 SNP coordinates
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.
Find the chromosome position for SNP ids, gene name or band
extraColumnSlotNames2-methods
~~ Methods for Function extraColumnSlotNames2 ~~
Access alleles for ChipInfo
Retreive GO terms from biomart for a given gene list
~~ Methods for Function coerce ~~
Convert from build 38 to build 37 SNP coordinates
Get human gene names and locations from biomart
Find closest SNPs to the ends of ranges
Autoimmune enriched regions as mapped on ImmunoChip
Meta-analysis using odds ratio and standard error from 2 datasets
Obtain a listing of known T1D associated genomic regions