Man pages for humarray
Simplify Analysis and Annotation of Human Microarray Datasets
| AB | Returns the A and B allele for SNP ids |
| allele-methods | Access alleles for ChipInfo |
| 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 |
| chipId-methods | Access chip-ids for ChipInfo |
| ChipInfo | Constructor (wrapper) for ChipInfo annotation object |
| ChipInfo-class | Class to represent SNP annotation for a microarray |
| ChipInfo-methods | rownames method for ChipInfo objects |
| ChipInfo-subset | Subset ChipInfo by chromosome |
| chip-methods | Retrieve the Chip name for ChipInfo |
| chip.support | Retrieve current ChipInfo annotation object |
| Chr | Find chromosome for SNP ids, gene name or band |
| chrIndices-methods | Chromosome indices method for ranged objects |
| chrInfo-methods | Chromosome info method for ranged objects |
| chrm-methods | Chromosome method for RangedData objects |
| chrNames-methods | Chromosome names method for ranged objects |
| chrNums | Extract chromosome numbers from GRanges/RangedData |
| chrSelect | Select chromosome subset of GRanges or RangedData object |
| chrSel-methods | Select chromosome subset for ranged objects |
| 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 |
| conv-methods | 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... |
| 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'... |
| extraColumnSlotNames2-methods | Get extra column slot names |
| 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... |
| get.telomere.locs | Derive Telomere locations across the genome |
| GRanges-methods | rownames method for GRanges objects |
| humarray-internal | Internal humarray Functions |
| humarray-package | Simplify Analysis and Annotation of Human Microarray Datasets |
| iChipRegionsB36 | Autoimmune enriched regions as mapped on ImmunoChip |
| ids.by.pos | Order rs-ids or ichip ids by chrosome and position |
| id.to.rs | Convert from chip ID labels to dbSNP rs-ids |
| ImmunoChipB37 | ImmunoChip annotation object (built-in) |
| invGRanges | Invert a ranged object Select the empty space between ranges... |
| in.window | Select all ranges lying within a chromosome window |
| lambda_1000 | Normalize Lambda inflation factors to specific case-control... |
| makeGRanges | Wrapper to construct GRanges object from chr,pos or... |
| manifest | Convert from chip/rs-ids to manifest chip ID labels |
| meta.me | Meta-analysis using odds ratio and standard error from 2... |
| nearest.gene | Retrieve the 'n' closest GENE labels or positions near... |
| nearest.snp | Retrieve the 'n' closest SNP ids or positions near specified... |
| plotGeneAnnot | Plot genes to annotate figures with genomic axes |
| plot-methods | Plot method for GRanges objects |
| plotRanges | Plot the locations specified in a GRanges or RangedData... |
| Pos | Find the chromosome position for SNP ids, gene name or band |
| Pos.band | Find the chromosome, start and end position for cytoband... |
| Pos.gene | Find the chromosome, start and end position for gene names |
| QC-methods | 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 |
| rangeSnp | Find closest SNPs to the starts and ends of ranges |
| recomWindow | Extend an interval or SNP by distance in centimorgans... |
| rranges | Simulate a GRanges or RangedData object |
| rs.id-methods | 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... |
| set.chr.to.char | Change the chromosome labels in a RangedData or GRanges... |
| set.chr.to.numeric | Change the chromosome labels in a RangedData or GRanges... |
| 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-methods | Retrieve the UCSC build for a ChipInfo object |
