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.
| Package: | humarray |
| Type: | humarray |
| Version: | 1.2 |
| Date: | 2017-11-17 |
| 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
NCmisc ~~
# NOT RUN {
#' randomly generated GRanges object
rranges()
# }
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