Simplify Analysis and Annotation of Human Microarray Datasets

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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.

Details

Package: humarray
Type: humarray
Version: 1.0.2
Date: 2016-07-12
License: GPL (>= 2)

This package helps to simplify common tasks in human genetics research, such as annotation lookup, conversion and labelling for GWAS analysis. Functions are provided that utilise GRanges, IRanges and data.frame (snpStats) objects for input and output. The new ChipInfo object, based on GRanges, once established, can provide seamless and automatic lookup for SNPs and their features within all functions, with no need to keep passing an object explicitly with each function call. By default, the annotation for immunoChip is built-in, but you can provide your own annotation for any chip to take its place. Intuitive wrappers are provided for annotation lookup (gene lists, exon ranges, cytobands, telomeres, etc) which take care of database lookup and download seamlessly in the background. Conversion between build 36 and 37 coordinates, with parameters required in most cases. New functions allow simple conversion between ensembl and HGNC gene labels, and chip specific ids to rs-ids for SNP-arrays. Simple function allow fast retrieval of chromosome and position for gene labels, karyotype bands or SNP-ids, or reverse lookup to see which features appear at, or nearest to a given location. There are randomisation functions to generate simulated GRanges and RangedData objects, lists of sample IDs and lists of SNP-ids.

List of functions ANNOTATION LOOKUP:

  • compact.gene.list Make a compact version of gene annotation

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

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

  • get.immunobase.snps Download GWAS hits from immunobase.org

  • 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 return subset of a ranged object that overlaps genes

  • get.GO.for.genes Retreive GO terms from biomart for a given gene list

  • get.immunog.locs Retrieve locations of Immunoglobin regions across the genome

  • get.recombination.map Get HapMap recombination rates for hg18 (build 36)

  • get.telomere.locs Derive Telomere locations across the genome

  • get.t1d.regions Obtain a listing of known T1D associated genomic regions

  • get.t1d.subset return subset of a ranged object that overlaps ichip dense mapped regions

  • nearest.gene Retrieve the 'n' closest GENE labels or positions near specified locus

  • plotGeneAnnot Plot genes to annotate figures with genomic axes

  • ucsc.sanitizer Standardize genome build string

RANGED DATA:

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

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

  • conv.36.37 Convert from build 36 to build 37 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

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

  • ranges.to.txt Convert GRanges/RangedData to chr:pos1-pos2 vector

  • select.autosomes Select ranges only within the 22 autosomes in a ranged data object

  • ranges.to.data.frame Convert RangedData/GRanges to a data.frame

  • data.frame.to.GRanges Convert a data.frame with positional information to GRanges

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

  • chrSel Select chromosome subset of GRanges or RangedData object

  • rranges Simulate a GRanges or RangedData object

  • chrNums Extract chromosome numbers from GRanges/RangedData

  • expand.nsnp Expand genomic locations to the ranges covering the 'n' closest SNPs

  • endSnp Find closest SNPs to the ends of ranges

  • rangeSnp Find closest SNPs to the starts and ends of ranges

  • startSnp Find closest SNPs to the starts of ranges

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

  • in.window Select all ranges lying within a chromosome window

  • plotRanges Plot the locations specified in a GRanges or RangedData 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

  • invGRanges Invert a ranged object

CHIP SUPPORT:

  • convert.textpos.to.data Convert a chr:pos1-pos2 vector to a matrix

  • chip.support Retrieve current ChipInfo annotation object

  • 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

  • rs.to.id Convert from dbSNP rs-ids to chip ID labels

  • get.nearby.snp.lists Obtain nearby SNP-lists within a recombination window

  • nearest.snp Retrieve the 'n' closest SNP ids or positions near specified locus

  • snps.in.range Retrieve SNP ids or positions in specified range

  • AB Returns the A and B allele for SNP ids

  • 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

  • Chr Find chromosome for SNP ids, gene name or band

  • Gene.pos Find the gene(s) overlapping a chromosome location

  • Pos Find the chromosome position for SNP ids, gene name or band

  • Pos.gene Find the chromosome, start and end position for gene names

  • Pos.band Find the chromosome, start and end position for cytoband names

Author(s)

Nicholas Cooper

Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>

See Also

NCmisc ~~

Examples

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#' randomly generated GRanges object
rranges()

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