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A B C D E F G H I L M N P Q R S U misc
| humarray-package | Simplify Analysis and Annotation of Human Microarray Datasets |
| A1 | Access alleles for ChipInfo |
| A1-method | Access alleles for ChipInfo |
| A1<- | Access alleles for ChipInfo |
| A1<--method | Access alleles for ChipInfo |
| A2 | Access alleles for ChipInfo |
| A2-method | Access alleles for ChipInfo |
| A2<- | Access alleles for ChipInfo |
| A2<--method | Access alleles for ChipInfo |
| AB | Returns the A and B allele for SNP ids |
| as | As("ChipInfo", "GRanges") |
| 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 |
| chip | Retrieve the Chip name for ChipInfo |
| chip-method | Retrieve the Chip name for ChipInfo |
| chip.support | Retrieve current ChipInfo annotation object |
| chipId | Access chip-ids for ChipInfo |
| chipId-method | Access chip-ids for ChipInfo |
| ChipInfo | Constructor (wrapper) for ChipInfo annotation object |
| ChipInfo-class | Class to represent SNP annotation for a microarray |
| ChipInfo-method | Class to represent SNP annotation for a microarray |
| Chr | Find chromosome for SNP ids, gene name or band |
| chrIndices-method | ~~ Methods for Function 'chrIndices' ~~ |
| chrIndices-methods | ~~ Methods for Function 'chrIndices' ~~ |
| chrInfo-method | ~~ Methods for Function 'chrInfo' ~~ |
| chrInfo-methods | ~~ Methods for Function 'chrInfo' ~~ |
| chrm | Chromosome method for RangedData objects |
| chrm-method | Chromosome method for RangedData objects |
| chrNames-method | ~~ Methods for Function 'chrNames' ~~ |
| chrNames-methods | ~~ Methods for Function 'chrNames' ~~ |
| chrNums | Extract chromosome numbers from GRanges/RangedData |
| chrSel | Select chromosome subset for ranged objects |
| chrSel-method | Select chromosome subset for ranged objects |
| chrSelect | Select chromosome subset of GRanges or RangedData object |
| coerce-method | ~~ Methods for Function 'coerce' ~~ |
| coerce-methods | ~~ Methods for Function 'coerce' ~~ |
| coerce<--method | ~~ 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 |
| convert.textpos.to.data | Convert a chr:pos1-pos2 vector to a matrix |
| convTo36 | Convert ChipInfo between build 36/37/38 coordinates |
| convTo36-method | Convert ChipInfo between build 36/37/38 coordinates |
| convTo37 | Convert ChipInfo between build 36/37/38 coordinates |
| convTo37-method | Convert ChipInfo between build 36/37/38 coordinates |
| convTo38 | Convert ChipInfo between build 36/37/38 coordinates |
| convTo38-method | Convert ChipInfo between build 36/37/38 coordinates |
| 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 |
| dim-method | rownames method for ChipInfo objects |
| endSnp | Find closest SNPs to the ends of ranges |
| ENS.to.GENE | Convert ensembl ids to HGNC gene ids |
| expand.nsnp | Expand genomic locations to the ranges covering the 'n' closest SNPs |
| extraColumnSlotNames2-method | ~~ Methods for Function 'extraColumnSlotNames2' ~~ |
| extraColumnSlotNames2-methods | ~~ Methods for Function 'extraColumnSlotNames2' ~~ |
| force.chr.pos | Force a valid genomic range, given the inputted coordinates |
| Gene.pos | Find the gene(s) overlapping a chromosome location |
| GENE.to.ENS | Convert gene ids to ensembl ids |
| 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.GO.for.genes | Retreive GO terms from biomart for a given gene list |
| 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 |
| GRanges | Plot method for GRanges objects |
| GRanges-method | Plot method for GRanges objects |
| humarray | 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 |
| ImmunoChipB37 | ImmunoChip annotation object (built-in) |
| in.window | Select all ranges lying within a chromosome window |
| initialize-method | Class to represent SNP annotation for a microarray |
| 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 |
| length-method | rownames method for ChipInfo objects |
| 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-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 |
| 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 |
| print-method | rownames method for ChipInfo objects |
| QCcode | Access quality control pass or fail codes for ChipInfo |
| QCcode-method | Access quality control pass or fail codes for ChipInfo |
| QCcode<- | Access quality control pass or fail codes for ChipInfo |
| QCcode<--method | Access quality control pass or fail codes for ChipInfo |
| QCfail | Access quality control pass or fail codes for ChipInfo |
| QCfail-method | Access quality control pass or fail codes for ChipInfo |
| QCpass | Access quality control pass or fail codes for ChipInfo |
| QCpass-method | Access quality control pass or fail codes for ChipInfo |
| ranged.to.data.frame | Convert RangedData/GRanges to a data.frame |
| ranged.to.txt | Convert GRanges/RangedData to chr:pos1-pos2 vector |
| RangedData | Plot method for GRanges objects |
| RangedData-method | Plot method for GRanges objects |
| rangeSnp | Find closest SNPs to the starts and ends of ranges |
| recomWindow | Extend an interval or SNP by distance in centimorgans (recombination distance) |
| rownames-method | rownames method for ChipInfo objects |
| rownames-method | rownames method for GRanges objects |
| rownames<--method | ~~ Methods for Function 'rownames<-' ~~ |
| rownames<--methods | ~~ Methods for Function 'rownames<-' ~~ |
| rranges | Simulate a GRanges or RangedData object |
| rs.id | Access rs-ids for ChipInfo |
| rs.id-method | 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 |
| show-method | rownames method for ChipInfo objects |
| 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 |
| ucsc-method | Retrieve the UCSC build for a ChipInfo object |
| [[-method | Subset ChipInfo by chromosome |