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humarray (version 1.2)

Simplify Analysis and Annotation of Human Microarray Datasets

Description

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.

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Version

Install

install.packages('humarray')

Monthly Downloads

40

Version

1.2

License

GPL (>= 2)

Maintainer

Nicholas Cooper

Last Published

November 20th, 2017

Functions in humarray (1.2)

[[,ChipInfo,ANY,ANY-method

Subset ChipInfo by chromosome
Band

Retrieve the cytoband(s) for snp ids, genes or locations
ChipInfo

Constructor (wrapper) for ChipInfo annotation object
ChipInfo-class

Class to represent SNP annotation for a microarray
rownames,GRanges-method

rownames method for GRanges objects
rownames,ChipInfo-method

rownames method for ChipInfo objects
Band.gene

Retrieve the cytoband(s) for genes labels
Pos.band

Find the chromosome, start and end position for cytoband names
chrNums

Extract chromosome numbers from GRanges/RangedData
Band.pos

Find the cytoband(s) overlapping a chromosome location
chrSel

Select chromosome subset for ranged objects
A1

Access alleles for ChipInfo
conv.36.37

Convert from build 36 to build 37 SNP coordinates
conv.37.36

Convert from build 37 to build 36 SNP coordinates
Pos.gene

Find the chromosome, start and end position for gene names
get.gene.annot

Get human gene names and locations from biomart
get.genic.subset

Obtain subset of ranged object overlapping human genes
GENE.to.ENS

Convert gene ids to ensembl ids
chip.support

Retrieve current ChipInfo annotation object
Chr

Find chromosome for SNP ids, gene name or band
convert.textpos.to.data

Convert a chr:pos1-pos2 vector to a matrix
df.to.GRanges

Convert a data.frame with positional information to GRanges
ENS.to.GENE

Convert ensembl ids to HGNC gene ids
expand.nsnp

Expand genomic locations to the ranges covering the 'n' closest SNPs
Pos

Find the chromosome position for SNP ids, gene name or band
extraColumnSlotNames2,ANY-method

Get extra column slot names
Gene.pos

Find the gene(s) overlapping a chromosome location
get.t1d.regions

Obtain a listing of known T1D associated genomic regions
ImmunoChipB37

ImmunoChip annotation object (built-in)
get.t1d.subset

Obtain subset of ranged object overlapping known T1D associated genomic regions
chip

Retrieve the Chip name for ChipInfo
get.telomere.locs

Derive Telomere locations across the genome
humarray-internal

Internal humarray Functions
chrInfo,RangedData-method

Chromosome info method for ranged objects
id.to.rs

Convert from chip ID labels to dbSNP rs-ids
chrNames,RangedData-method

Chromosome names method for ranged objects
ids.by.pos

Order rs-ids or ichip ids by chrosome and position
conv.37.38

Convert from build 37 to build 38 SNP coordinates
get.centromere.locs

Return Centromere locations across the genome
get.chr.lens

Get chromosome lengths from build database
conv.38.37

Convert from build 38 to build 37 SNP coordinates
get.nearby.snp.lists

Obtain nearby SNP-lists within a recombination window
get.recombination.map

Get HapMap recombination rates for hg18 (build 36)
plot,GRanges,ANY-method

Plot method for GRanges objects
nearest.gene

Retrieve the 'n' closest GENE labels or positions near specified locus
plotGeneAnnot

Plot genes to annotate figures with genomic axes
ucsc

Retrieve the UCSC build for a ChipInfo object
nearest.snp

Retrieve the 'n' closest SNP ids or positions near specified locus
plotRanges

Plot the locations specified in a GRanges or RangedData object
as

As("ChipInfo", "GRanges")
rangeSnp

Find closest SNPs to the starts and ends of ranges
chrSelect

Select chromosome subset of GRanges or RangedData object
force.chr.pos

Force a valid genomic range, given the inputted coordinates
chrm

Chromosome method for RangedData objects
get.GO.for.genes

Retreive GO terms from biomart for a given gene list
compact.gene.list

Make a compact version of gene annotation
humarray-package

Simplify Analysis and Annotation of Human Microarray Datasets
iChipRegionsB36

Autoimmune enriched regions as mapped on ImmunoChip
convTo37

Convert ChipInfo between build 36/37/38 coordinates
lambda_1000

Normalize Lambda inflation factors to specific case-control count
QCcode

Access quality control pass or fail codes for ChipInfo
makeGRanges

Wrapper to construct GRanges object from chr,pos or chr,start,end
chipId

Access chip-ids for ChipInfo
in.window

Select all ranges lying within a chromosome window
chrIndices,RangedData-method

Chromosome indices method for ranged objects
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.
rs.id

Access rs-ids for ChipInfo
df.to.ranged

Convert a data.frame with positional information to RangedData/GRanges
ranged.to.data.frame

Convert RangedData/GRanges to a data.frame
rs.to.id

Convert from dbSNP rs-ids to chip ID labels
ranged.to.txt

Convert GRanges/RangedData to chr:pos1-pos2 vector
select.autosomes

Select ranges only within the 22 autosomes in a ranged data object
snps.in.range

Retrieve SNP ids or positions in specified range
set.chr.to.char

Change the chromosome labels in a RangedData or GRanges object to string codes
endSnp

Find closest SNPs to the ends of ranges
get.immunobase.snps

Download GWAS hits from t1dbase.org
get.cyto

Return Cytoband/Karyotype locations across the genome
get.immunog.locs

Retrieve locations of Immunoglobin regions across the genome
get.exon.annot

Get exon names and locations from UCSC
startSnp

Find closest SNPs to the starts of ranges
manifest

Convert from chip/rs-ids to manifest chip ID labels
rranges

Simulate a GRanges or RangedData object
meta.me

Meta-analysis using odds ratio and standard error from 2 datasets
set.chr.to.numeric

Change the chromosome labels in a RangedData or GRanges object to numbers
recomWindow

Extend an interval or SNP by distance in centimorgans (recombination distance)
showChipInfo

Display a ChipInfo object
AB

Returns the A and B allele for SNP ids