Man pages for humarray
Simplify Analysis and Annotation of Human Microarray Datasets

ABReturns the A and B allele for SNP ids
allele-methodsAccess alleles for ChipInfo
asAs("ChipInfo", "GRanges")
BandRetrieve the cytoband(s) for snp ids, genes or locations
Band.geneRetrieve the cytoband(s) for genes labels
Band.posFind the cytoband(s) overlapping a chromosome location
chipId-methodsAccess chip-ids for ChipInfo
ChipInfoConstructor (wrapper) for ChipInfo annotation object
ChipInfo-classClass to represent SNP annotation for a microarray
ChipInfo-methodsrownames method for ChipInfo objects
ChipInfo-subsetSubset ChipInfo by chromosome
chip-methodsRetrieve the Chip name for ChipInfo
chip.supportRetrieve current ChipInfo annotation object
ChrFind chromosome for SNP ids, gene name or band
chrIndices-methodsChromosome indices method for ranged objects
chrInfo-methodsChromosome info method for ranged objects
chrm-methodsChromosome method for RangedData objects
chrNames-methodsChromosome names method for ranged objects
chrNumsExtract chromosome numbers from GRanges/RangedData
chrSelectSelect chromosome subset of GRanges or RangedData object
chrSel-methodsSelect chromosome subset for ranged objects
compact.gene.listMake a compact version of gene annotation
conv.36.37Convert from build 36 to build 37 SNP coordinates
conv.37.36Convert from build 37 to build 36 SNP coordinates
conv.37.38Convert from build 37 to build 38 SNP coordinates
conv.38.37Convert from build 38 to build 37 SNP coordinates a chr:pos1-pos2 vector to a matrix
conv-methodsConvert ChipInfo between build 36/37/38 coordinates a data.frame with positional information to GRanges a data.frame with positional information to...
endSnpFind closest SNPs to the ends of ranges ensembl ids to HGNC gene ids
expand.nsnpExpand genomic locations to the ranges covering the 'n'...
extraColumnSlotNames2-methodsGet extra column slot names
force.chr.posForce a valid genomic range, given the inputted coordinates
Gene.posFind the gene(s) overlapping a chromosome location gene ids to ensembl ids
get.centromere.locsReturn Centromere locations across the genome
get.chr.lensGet chromosome lengths from build database
get.cytoReturn Cytoband/Karyotype locations across the genome
get.exon.annotGet exon names and locations from UCSC
get.gene.annotGet human gene names and locations from biomart
get.genic.subsetObtain subset of ranged object overlapping human genes
get.GO.for.genesRetreive GO terms from biomart for a given gene list
get.immunobase.snpsDownload GWAS hits from
get.immunog.locsRetrieve locations of Immunoglobin regions across the genome
get.nearby.snp.listsObtain nearby SNP-lists within a recombination window
get.recombination.mapGet HapMap recombination rates for hg18 (build 36)
get.t1d.regionsObtain a listing of known T1D associated genomic regions
get.t1d.subsetObtain subset of ranged object overlapping known T1D...
get.telomere.locsDerive Telomere locations across the genome
GRanges-methodsrownames method for GRanges objects
humarray-internalInternal humarray Functions
humarray-packageSimplify Analysis and Annotation of Human Microarray Datasets
iChipRegionsB36Autoimmune enriched regions as mapped on ImmunoChip rs-ids or ichip ids by chrosome and position from chip ID labels to dbSNP rs-ids
ImmunoChipB37ImmunoChip annotation object (built-in)
invGRangesInvert a ranged object Select the empty space between ranges...
in.windowSelect all ranges lying within a chromosome window
lambda_1000Normalize Lambda inflation factors to specific case-control...
makeGRangesWrapper to construct GRanges object from chr,pos or...
manifestConvert from chip/rs-ids to manifest chip ID labels
meta.meMeta-analysis using odds ratio and standard error from 2...
nearest.geneRetrieve the 'n' closest GENE labels or positions near...
nearest.snpRetrieve the 'n' closest SNP ids or positions near specified...
plotGeneAnnotPlot genes to annotate figures with genomic axes
plot-methodsPlot method for GRanges objects
plotRangesPlot the locations specified in a GRanges or RangedData...
PosFind the chromosome position for SNP ids, gene name or band
Pos.bandFind the chromosome, start and end position for cytoband...
Pos.geneFind the chromosome, start and end position for gene names
QC-methodsAccess quality control pass or fail codes for ChipInfo RangedData/GRanges to a data.frame GRanges/RangedData to chr:pos1-pos2 vector
rangeSnpFind closest SNPs to the starts and ends of ranges
recomWindowExtend an interval or SNP by distance in centimorgans...
rrangesSimulate a GRanges or RangedData object rs-ids for ChipInfo from dbSNP rs-ids to chip ID labels
select.autosomesSelect ranges only within the 22 autosomes in a ranged data... the chromosome labels in a RangedData or GRanges... the chromosome labels in a RangedData or GRanges...
showChipInfoDisplay a ChipInfo object SNP ids or positions in specified range
startSnpFind closest SNPs to the starts of ranges
ucsc-methodsRetrieve the UCSC build for a ChipInfo object
humarray documentation built on Nov. 20, 2017, 1:05 a.m.