gscores {GenomicScores} | R Documentation |
Functions to access genomic gscores through GScores
objects.
availableGScores() getGScores(x) ## S4 method for signature 'GScores,GenomicRanges' gscores(x, ranges, ...) ## S4 method for signature 'GScores,character' gscores(x, ranges, ...) ## S4 method for signature 'MafDb,GenomicRanges' gscores(x, ranges, ...) ## S4 method for signature 'GScores' score(x, ..., simplify=TRUE) ## S4 method for signature 'MafDb' score(x, ..., simplify=TRUE)
x |
For |
ranges |
A |
... |
In the call to the
|
simplify |
Flag setting whether the result should be simplified to a
vector ( |
The function availableGScores()
shows genomic score sets available as
AnnotationHub
online resources.
The method gscores()
takes as first argument a GScores-class
object that can be loaded from an annotation package or from an
AnnotationHub
resource. These two possibilities are illustrated in the
examples below.
The function availableGScores()
returns a character vector with the
names of the AnnotationHub
resources corresponding to different
available sets of genomic scores. The function getGScores()
return a
GScores
object. The method gscores()
returns a GRanges
object with the genomic scores in a metadata column called score
.
The method score()
returns a numeric vector with the genomic scores.
R. Castelo
phastCons100way.UCSC.hg19
MafDb.1Kgenomes.phase1.hs37d5
## one genomic range of width 5 gr1 <- GRanges(seqnames="chr7", IRanges(start=117232380, width=5)) gr1 ## five genomic ranges of width 1 gr2 <- GRanges(seqnames="chr7", IRanges(start=117232380:117232384, width=1)) gr2 ## accessing genomic gscores from an annotation package if (require(phastCons100way.UCSC.hg19)) { library(GenomicRanges) gsco <- phastCons100way.UCSC.hg19 gsco gscores(gsco, gr1) score(gsco, gr1) gscores(gsco, gr2) populations(gsco) gscores(gsco, gr2, pop="DP2") } if (require(MafDb.1Kgenomes.phase1.hs37d5)) { mafdb <- MafDb.1Kgenomes.phase1.hs37d5 mafdb populations(mafdb) ## lookup allele frequencies for SNP rs1129038, located at 15:28356859, a ## SNP associated to blue and brown eye colors as reported by Eiberg et al. ## Blue eye color in humans may be caused by a perfectly associated founder ## mutation in a regulatory element located within the HERC2 gene ## inhibiting OCA2 expression. Human Genetics, 123(2):177-87, 2008 ## [http://www.ncbi.nlm.nih.gov/pubmed/18172690] gscores(mafdb, GRanges("15:28356859"), pop=populations(mafdb)) gscores(mafdb, "rs1129038", pop=populations(mafdb)) } ## accessing genomic scores from AnnotationHub resources ## Not run: availableGScores() gsco <- getGScores("phastCons100way.UCSC.hg19") gscores(gsco, gr1) ## End(Not run)