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

Functions

A1 Man page
A1<- Man page
A1<-,ChipInfo-method Man page
A1,ChipInfo-method Man page
A2 Man page
A2<- Man page
A2<-,ChipInfo-method Man page
A2,ChipInfo-method Man page
AB Man page
add.trail Man page
as Man page
Band Man page
Band.gene Man page
Band.pos Man page
chip Man page
chip,ChipInfo-method Man page
chipId Man page
chipId,ChipInfo-method Man page
ChipInfo Man page
[[,ChipInfo,ANY,ANY-method Man page
ChipInfo-class Man page
ChipInfo-method Man page
chip.support Man page
Chr Man page
chr2 Man page
chrGS Man page
chrIndices2 Man page
chrIndicesGS Man page
chrIndices-methods Man page
chrIndices,RangedData-method Man page
chrInfo2 Man page
chrInfoGS Man page
chrInfo-methods Man page
chrInfo,RangedData-method Man page
chrm Man page
chrm,ChipInfo-method Man page
chrm,GRanges-method Man page
chrm,RangedData-method Man page
chrNames2 Man page
chrNames-methods Man page
chrNames,RangedData-method Man page
chrnames.to.num Man page
chrNums Man page
chrnums.to.txt Man page
chrOrder2 Man page
chrPartitioning2 Man page
chrSel Man page
chrSel,ChipInfo-method Man page
chrSelect Man page
chrSel,GRanges-method Man page
chrSel,RangedData-method Man page
clean.snp.ids Man page
coerce,ChipInfo,data.frame-method Man page
coerce<-,ChipInfo,GRanges-method Man page
coerce,ChipInfo,GRanges-method Man page
coerce,ChipInfo,RangedData-method Man page
coerce,data.frame,ChipInfo-method Man page
coerce,data.frame,GRanges-method Man page
coerce,data.frame,RangedData-method Man page
coerce,GRanges,ChipInfo-method Man page
coerce,GRanges,data.frame-method Man page
coerce<--methods Man page
coerce-methods Man page
coerce,RangedData,ChipInfo-method Man page
coerce,RangedData,data.frame-method Man page
comma Man page
compact.gene.list Man page
conv.36.37 Man page
conv.37.36 Man page
conv.37.38 Man page
conv.38.37 Man page
convert.textpos.to.data Man page
convTo36 Man page
convTo36,ChipInfo-method Man page
convTo37 Man page
convTo37,ChipInfo-method Man page
convTo38 Man page
convTo38,ChipInfo-method Man page
Cor Man page
df.to.GRanges Man page
df.to.ranged Man page
dim,ChipInfo-method Man page
do.cw Man page
egSymb Man page
emd.rmv Man page
endSnp Man page
ENS.to.GENE Man page
expand.nsnp Man page
extraColumnSlotNames2 Man page
extraColumnSlotNames2,ANY-method Man page
extraColumnSlotNames2-methods Man page
extraColumnSlots2 Man page
finitize Man page
force.chr.pos Man page
gene.duplicate.report Man page
Gene.pos Man page
GENE.to.ENS Man page
get.centromere.locs Man page
get.chr.lens Man page
get.cyto Man page
get.exon.annot Man page
get.gene.annot Man page
get.genic.subset Man page
get.GO.for.genes Man page
get.immunobase.snps Man page
get.immunog.locs Man page
get.nearby.snp.lists Man page
get.recombination.map Man page
get.t1d.regions Man page
get.t1d.subset Man page
get.telomere.locs Man page
GRanges Man page
GRanges-method Man page
hard.coded.conv Man page
hg18ToHg19 Man page
hg19ToHg18 Man page
hg19ToHg38 Man page
hg38ToHg19 Man page
humarray Man page
humarray-package Man page
iChipRegionsB36 Man page
ids.by.pos Man page
id.to.rs Man page
immunobase.has.changed Man page
ImmunoChipB37 Man page
initialize,ChipInfo-method Man page
invGRanges Man page
in.window Man page
l10 Man page
lambda_1000 Man page
length,ChipInfo-method Man page
make.divisor Man page
makeGRanges Man page
.makeNakedMatFromChipInfo Man page
makePrettyMatrixForCompactPrinting2 Man page
manifest Man page
maxna Man page
meanna Man page
medianna Man page
meta.me Man page
minna Man page
nearest.gene Man page
nearest.snp Man page
order.chr Man page
pduplicated Man page
plotdf Man page
plotGeneAnnot Man page
plot.get.area Man page
plot,GRanges,ANY-method Man page
plot,RangedData,ANY-method Man page
plotRanges Man page
Pos Man page
Pos.band Man page
Pos.gene Man page
print,ChipInfo-method Man page
pt2 Man page
QCcode Man page
QCcode<- Man page
QCcode<-,ChipInfo-method Man page
QCcode,ChipInfo-method Man page
QCfail Man page
QCfail,ChipInfo-method Man page
QCpass Man page
QCpass,ChipInfo-method Man page
RangedData Man page
RangedData-method Man page
ranged.to.data.frame Man page
ranged.to.txt Man page
rangeSnp Man page
recomWindow Man page
rmv.trail Man page
.rownames3 Man page
rownames,ChipInfo-method Man page
rownames<-,GRanges-method Man page
rownames,GRanges-method Man page
rownames<--methods Man page
rranges Man page
rsampid Man page
rs.id Man page
rs.id,ChipInfo-method Man page
rsnpid Man page
rs.to.id Man page
sdna Man page
select.autosomes Man page
set.chr.to.char Man page
set.chr.to.numeric Man page
showChipInfo Man page
show,ChipInfo-method Man page
snps.in.range Man page
sort.chr Man page
sortna Man page
startSnp Man page
substitute.36s Man page
sumna Man page
TGOGR Man page
TGORD Man page
tidy.extra.chr Man page
toGenomeOrder2 Man page
ucsc Man page
ucsc,ChipInfo-method Man page
ucsc.sanitizer Man page
.updateAllele Man page
validate.dir.for Man page

Files

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

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