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humarray (version 1.0.0)

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

10

Version

1.0.0

License

GPL (>= 2)

Maintainer

Nicholas Cooper

Last Published

March 3rd, 2016

Functions in humarray (1.0.0)

Pos.gene

Find the chromosome, start and end position for gene names
df.to.ranged

Convert a data.frame with positional information to RangedData/GRanges
convTo37

Convert ChipInfo between build 36/37/38 coordinates
set.chr.to.char

Change the chromosome labels in a RangedData or GRanges object to string codes
get.genic.subset

Obtain subset of ranged object overlapping human genes
in.window

Select all ranges lying within a chromosome window
toGenomeOrder-methods

~~ Methods for Function toGenomeOrder ~~
snps.in.range

Retrieve SNP ids or positions in specified range
Band.pos

Find the cytoband(s) overlapping a chromosome location
chipId

Access chip-ids for ChipInfo
chrInfo-methods

~~ Methods for Function chrInfo ~~
conv.36.37

Convert from build 36 to build 37 SNP coordinates
get.exon.annot

Get exon names and locations from UCSC
get.nearby.snp.lists

Obtain nearby SNP-lists within a recombination window
ids.by.pos

Order rs-ids or ichip ids by chrosome and position
plot,GRanges,ANY-method

Plot method for GRanges objects
rs.id

Access rs-ids for ChipInfo
ENS.to.GENE

Convert ensembl ids to HGNC gene ids
GENE.to.ENS

Convert gene ids to ensembl ids
chrSel

Select chromosome subset for ranged objects
compact.gene.list

Make a compact version of gene annotation
expand.nsnp

Expand genomic locations to the ranges covering the 'n' closest SNPs
nearest.gene

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

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

Simulate a GRanges or RangedData object
showChipInfo

Display a ChipInfo object
chip

Retrieve the Chip name for ChipInfo
df.to.GRanges

Convert a data.frame with positional information to GRanges
rownames<--methods

~~ Methods for Function rownames<- ~~
get.chr.lens

Get chromosome lengths from build database
ucsc

Retrieve the UCSC build for a ChipInfo object
startSnp

Find closest SNPs to the starts of ranges
get.t1d.subset

Obtain subset of ranged object overlapping known T1D associated genomic regions
rownames,ChipInfo-method

rownames method for ChipInfo objects
ChipInfo-class

Class to represent SNP annotation for a microarray
Band.gene

Retrieve the cytoband(s) for genes labels
Chr

Find chromosome for SNP ids, gene name or band
QCcode

Access quality control pass or fail codes for ChipInfo
chrNums

Extract chromosome numbers from GRanges/RangedData
conv.37.36

Convert from build 37 to build 36 SNP coordinates
convert.textpos.to.data

Convert a chr:pos1-pos2 vector to a matrix
humarray-internal

Internal humarray Functions
rs.to.id

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

Convert RangedData/GRanges to a data.frame
chrm

Chromosome method for RangedData objects
lambda_1000

Normalize Lambda inflation factors to specific case-control count
plotGeneAnnot

Plot genes to annotate figures with genomic axes
set.chr.to.numeric

Change the chromosome labels in a RangedData or GRanges object to numbers
get.cyto

Return Cytoband/Karyotype locations across the genome
ImmunoChipB37

ImmunoChip annotation object (built-in)
coerce<--methods

~~ Methods for Function coerce<- ~~
chip.support

Retrieve current ChipInfo annotation object
get.immunobase.snps

Download GWAS hits from t1dbase.org
id.to.rs

Convert from chip ID labels to dbSNP rs-ids
humarray-package

Simplify Analysis and Annotation of Human Microarray Datasets
recomWindow

Extend an interval or SNP by distance in centimorgans (recombination distance)
Gene.pos

Find the gene(s) overlapping a chromosome location
as

As("ChipInfo", "GRanges")
chrNames-methods

~~ Methods for Function chrNames ~~
chrIndices-methods

~~ Methods for Function chrIndices ~~
force.chr.pos

Force a valid genomic range, given the inputted coordinates
get.recombination.map

Get HapMap recombination rates for hg18 (build 36)
get.centromere.locs

Return Centromere locations across the genome
select.autosomes

Select ranges only within the 22 autosomes in a ranged data object
nearest.snp

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

Find closest SNPs to the starts and ends of ranges
AB

Returns the A and B allele for SNP ids
[[,ChipInfo,ANY,ANY-method

Subset ChipInfo by chromosome
get.immunog.locs

Retrieve locations of Immunoglobin regions across the genome
get.telomere.locs

Derive Telomere locations across the genome
chrSelect

Select chromosome subset of GRanges or RangedData object
plotRanges

Plot the locations specified in a GRanges or RangedData object
manifest

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

Convert GRanges/RangedData to chr:pos1-pos2 vector
rownames,GRanges-method

rownames method for GRanges objects
ChipInfo

Constructor (wrapper) for ChipInfo annotation object
Band

Retrieve the cytoband(s) for snp ids, genes or locations
Pos.band

Find the chromosome, start and end position for cytoband names
conv.37.38

Convert from build 37 to build 38 SNP coordinates
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.
Pos

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

~~ Methods for Function extraColumnSlotNames2 ~~
A1

Access alleles for ChipInfo
get.GO.for.genes

Retreive GO terms from biomart for a given gene list
coerce-methods

~~ Methods for Function coerce ~~
conv.38.37

Convert from build 38 to build 37 SNP coordinates
get.gene.annot

Get human gene names and locations from biomart
endSnp

Find closest SNPs to the ends of ranges
iChipRegionsB36

Autoimmune enriched regions as mapped on ImmunoChip
meta.me

Meta-analysis using odds ratio and standard error from 2 datasets
get.t1d.regions

Obtain a listing of known T1D associated genomic regions