humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Utilises GRanges, data.frame or IRanges objects. Integrates gene annotation for ImmunoChip (or your custom chip) with function calls. Intuitive wrappers for annotation lookup (gene lists, exon ranges, etc) and conversion (e.g, between build 36 and 37 coordinates). Conversion between ensembl and HGNC gene ids, chip ids to rs-ids for SNP-arrays. Retrieval of chromosome and position for gene, band or SNP-ids, or reverse lookup. Simulation functions for ranges objects.

AuthorNicholas Cooper
Date of publication2017-01-09 09:49:50
MaintainerNicholas Cooper <njcooper@gmx.co.uk>
LicenseGPL (>= 2)
Version1.1

View on CRAN

Man pages

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: ~~ Methods for Function 'chrIndices' ~~

chrInfo-methods: ~~ Methods for Function 'chrInfo' ~~

chrm-methods: Chromosome method for RangedData objects

chrNames-methods: ~~ Methods for Function 'chrNames' ~~

chrNums: Extract chromosome numbers from GRanges/RangedData

chrSelect: Select chromosome subset of GRanges or RangedData object

chrSel-methods: Select chromosome subset for ranged 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

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: ~~ 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...

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...

rownames_--methods: ~~ Methods for Function 'rownames<-' ~~

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

Files in this package

humarray
humarray/NAMESPACE
humarray/data
humarray/data/hg38ToHg19.rda
humarray/data/ImmunoChipB37.rda
humarray/data/datalist
humarray/data/hg19ToHg18.rda
humarray/data/hg19ToHg38.rda
humarray/data/iChipRegionsB36.rda
humarray/data/hg18ToHg19.rda
humarray/data/egSymb.rda
humarray/R
humarray/R/humarray_datasets.R humarray/R/humarray.R
humarray/MD5
humarray/DESCRIPTION
humarray/man
humarray/man/expand.nsnp.Rd humarray/man/get.chr.lens.Rd humarray/man/endSnp.Rd humarray/man/Band.gene.Rd humarray/man/chrIndices-methods.Rd humarray/man/Pos.gene.Rd humarray/man/conv.37.38.Rd humarray/man/startSnp.Rd humarray/man/plot-methods.Rd humarray/man/lambda_1000.Rd humarray/man/id.to.rs.Rd humarray/man/recomWindow.Rd humarray/man/rs.to.id.Rd humarray/man/df.to.GRanges.Rd humarray/man/chrSel-methods.Rd humarray/man/select.autosomes.Rd humarray/man/get.recombination.map.Rd humarray/man/ENS.to.GENE.Rd humarray/man/ucsc-methods.Rd humarray/man/Band.pos.Rd humarray/man/get.nearby.snp.lists.Rd humarray/man/get.t1d.regions.Rd humarray/man/ChipInfo-methods.Rd humarray/man/chrNames-methods.Rd humarray/man/makeGRanges.Rd humarray/man/get.GO.for.genes.Rd humarray/man/nearest.snp.Rd humarray/man/iChipRegionsB36.Rd humarray/man/chrm-methods.Rd humarray/man/Pos.Rd humarray/man/chrInfo-methods.Rd humarray/man/meta.me.Rd humarray/man/conv.38.37.Rd humarray/man/GRanges-methods.Rd humarray/man/nearest.gene.Rd humarray/man/showChipInfo.Rd humarray/man/ranged.to.txt.Rd humarray/man/get.t1d.subset.Rd humarray/man/get.centromere.locs.Rd humarray/man/rs.id-methods.Rd humarray/man/get.cyto.Rd humarray/man/compact.gene.list.Rd humarray/man/Gene.pos.Rd humarray/man/extraColumnSlotNames2-methods.Rd humarray/man/ImmunoChipB37.Rd humarray/man/conv.37.36.Rd humarray/man/ids.by.pos.Rd humarray/man/ranged.to.data.frame.Rd humarray/man/ChipInfo-subset.Rd humarray/man/QC-methods.Rd humarray/man/df.to.ranged.Rd humarray/man/chipId-methods.Rd humarray/man/humarray-package.Rd humarray/man/Pos.band.Rd humarray/man/humarray-internal.Rd humarray/man/invGRanges.Rd humarray/man/conv-methods.Rd humarray/man/chrNums.Rd humarray/man/conv.36.37.Rd humarray/man/rranges.Rd humarray/man/coerce-methods.Rd humarray/man/force.chr.pos.Rd humarray/man/snps.in.range.Rd humarray/man/set.chr.to.numeric.Rd humarray/man/in.window.Rd humarray/man/rangeSnp.Rd humarray/man/convert.textpos.to.data.Rd humarray/man/rownames_--methods.Rd humarray/man/get.gene.annot.Rd humarray/man/get.immunog.locs.Rd humarray/man/get.exon.annot.Rd humarray/man/allele-methods.Rd humarray/man/get.telomere.locs.Rd humarray/man/Chr.Rd humarray/man/ChipInfo-class.Rd humarray/man/AB.Rd humarray/man/get.immunobase.snps.Rd humarray/man/chip-methods.Rd humarray/man/set.chr.to.char.Rd humarray/man/get.genic.subset.Rd humarray/man/manifest.Rd humarray/man/chip.support.Rd humarray/man/Band.Rd humarray/man/coerce_--methods.Rd humarray/man/GENE.to.ENS.Rd humarray/man/ChipInfo.Rd humarray/man/plotRanges.Rd humarray/man/chrSelect.Rd humarray/man/as.Rd humarray/man/plotGeneAnnot.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.