humarray: Simplify Analysis and Annotation of Human Microarray Datasets

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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.

Author
Nicholas Cooper
Date of publication
2016-07-15 14:37:12
Maintainer
Nicholas Cooper <njcooper@gmx.co.uk>
License
GPL (>= 2)
Version
1.0.2

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