# Simplify Analysis and Annotation of Human Microarray Datasets

## Documentation for package ‘humarray’ version 1.1

- DESCRIPTION file.

## Help Pages

A B C D E F G H I L M N P Q R S U misc

humarray-package | Simplify Analysis and Annotation of Human Microarray Datasets

## -- A --

A1 | Access alleles for ChipInfo
A1-method | Access alleles for ChipInfo
A1<- | Access alleles for ChipInfo
A1<--method | Access alleles for ChipInfo
A2 | Access alleles for ChipInfo
A2-method | Access alleles for ChipInfo
A2<- | Access alleles for ChipInfo
A2<--method | Access alleles for ChipInfo
AB | Returns the A and B allele for SNP ids
as | As("ChipInfo", "GRanges")

## -- B --

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

## -- C --

chip | Retrieve the Chip name for ChipInfo
chip-method | Retrieve the Chip name for ChipInfo
chip.support | Retrieve current ChipInfo annotation object
chipId | Access chip-ids for ChipInfo
chipId-method | Access chip-ids for ChipInfo
ChipInfo | Constructor (wrapper) for ChipInfo annotation object
ChipInfo-class | Class to represent SNP annotation for a microarray
ChipInfo-method | Class to represent SNP annotation for a microarray
Chr | Find chromosome for SNP ids, gene name or band
chrIndices-method | ~~ Methods for Function 'chrIndices' ~~
chrIndices-methods | ~~ Methods for Function 'chrIndices' ~~
chrInfo-method | ~~ Methods for Function 'chrInfo' ~~
chrInfo-methods | ~~ Methods for Function 'chrInfo' ~~
chrm | Chromosome method for RangedData objects
chrm-method | Chromosome method for RangedData objects
chrNames-method | ~~ Methods for Function 'chrNames' ~~
chrNames-methods | ~~ Methods for Function 'chrNames' ~~
chrNums | Extract chromosome numbers from GRanges/RangedData
chrSel | Select chromosome subset for ranged objects
chrSel-method | Select chromosome subset for ranged objects
chrSelect | Select chromosome subset of GRanges or RangedData object
coerce-method | ~~ Methods for Function 'coerce' ~~
coerce-methods | ~~ Methods for Function 'coerce' ~~
coerce<--method | ~~ 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
convTo36 | Convert ChipInfo between build 36/37/38 coordinates
convTo36-method | Convert ChipInfo between build 36/37/38 coordinates
convTo37 | Convert ChipInfo between build 36/37/38 coordinates
convTo37-method | Convert ChipInfo between build 36/37/38 coordinates
convTo38 | Convert ChipInfo between build 36/37/38 coordinates
convTo38-method | Convert ChipInfo between build 36/37/38 coordinates

## -- D --

df.to.GRanges | Convert a data.frame with positional information to GRanges
df.to.ranged | Convert a data.frame with positional information to RangedData/GRanges
dim-method | rownames method for ChipInfo objects

## -- E --

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' closest SNPs
extraColumnSlotNames2-method | ~~ Methods for Function 'extraColumnSlotNames2' ~~
extraColumnSlotNames2-methods | ~~ Methods for Function 'extraColumnSlotNames2' ~~

## -- F --

force.chr.pos | Force a valid genomic range, given the inputted coordinates

## -- G --

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 associated genomic regions
get.telomere.locs | Derive Telomere locations across the genome
GRanges | Plot method for GRanges objects
GRanges-method | Plot method for GRanges objects

## -- H --

humarray | Simplify Analysis and Annotation of Human Microarray Datasets

## -- I --

iChipRegionsB36 | Autoimmune enriched regions as mapped on ImmunoChip
id.to.rs | Convert from chip ID labels to dbSNP rs-ids
ids.by.pos | Order rs-ids or ichip ids by chrosome and position
ImmunoChipB37 | ImmunoChip annotation object (built-in)
in.window | Select all ranges lying within a chromosome window
initialize-method | Class to represent SNP annotation for a microarray
invGRanges | Invert a ranged object Select the empty space between ranges for the whole genome, for instance you may want to overlap with everything NOT in a set of ranges.

## -- L --

lambda_1000 | Normalize Lambda inflation factors to specific case-control count
length-method | rownames method for ChipInfo objects

## -- M --

makeGRanges | Wrapper to construct GRanges object from chr,pos or chr,start,end
manifest | Convert from chip/rs-ids to manifest chip ID labels
meta.me | Meta-analysis using odds ratio and standard error from 2 datasets

## -- N --

nearest.gene | Retrieve the 'n' closest GENE labels or positions near specified locus
nearest.snp | Retrieve the 'n' closest SNP ids or positions near specified locus

## -- P --

plot-method | Plot method for GRanges objects
plotGeneAnnot | Plot genes to annotate figures with genomic axes
plotRanges | Plot the locations specified in a GRanges or RangedData object
Pos | Find the chromosome position for SNP ids, gene name or band
Pos.band | Find the chromosome, start and end position for cytoband names
Pos.gene | Find the chromosome, start and end position for gene names
print-method | rownames method for ChipInfo objects

## -- Q --

QCcode | Access quality control pass or fail codes for ChipInfo
QCcode-method | Access quality control pass or fail codes for ChipInfo
QCcode<- | Access quality control pass or fail codes for ChipInfo
QCcode<--method | Access quality control pass or fail codes for ChipInfo
QCfail | Access quality control pass or fail codes for ChipInfo
QCfail-method | Access quality control pass or fail codes for ChipInfo
QCpass | Access quality control pass or fail codes for ChipInfo
QCpass-method | Access quality control pass or fail codes for ChipInfo

## -- R --

ranged.to.data.frame | Convert RangedData/GRanges to a data.frame
ranged.to.txt | Convert GRanges/RangedData to chr:pos1-pos2 vector
RangedData | Plot method for GRanges objects
RangedData-method | Plot method for GRanges objects
rangeSnp | Find closest SNPs to the starts and ends of ranges
recomWindow | Extend an interval or SNP by distance in centimorgans (recombination distance)
rownames-method | rownames method for ChipInfo objects
rownames-method | rownames method for GRanges objects
rownames<--method | ~~ Methods for Function 'rownames<-' ~~
rownames<--methods | ~~ Methods for Function 'rownames<-' ~~
rranges | Simulate a GRanges or RangedData object
rs.id | Access rs-ids for ChipInfo
rs.id-method | Access rs-ids for ChipInfo
rs.to.id | Convert from dbSNP rs-ids to chip ID labels

## -- S --

select.autosomes | Select ranges only within the 22 autosomes in a ranged data object
set.chr.to.char | Change the chromosome labels in a RangedData or GRanges object to string codes
set.chr.to.numeric | Change the chromosome labels in a RangedData or GRanges object to numbers
show-method | rownames method for ChipInfo objects
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

## -- U --

ucsc | Retrieve the UCSC build for a ChipInfo object
ucsc-method | Retrieve the UCSC build for a ChipInfo object

## -- misc --

[[-method | Subset ChipInfo by chromosome