Find SNPs which belongs to alternative exons and flanking introns of them.

Description

Find SNPs which belong to alternative exons and flanking introns of them.

Usage

findOversnp(altInvalue = NULL, snprange = NULL)

Arguments

Value

This function returns a matrix with SNPs in alternative exons and flanking introns and ranges of those SNPs.

Author(s)

Seonggyun Han, Sangsoo Kim

See Also

findOverlaps

Examples

sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
sample.Txdb <- loadDb(sampleDB)
data(samplesnplocus)
data(samplesnp)
filtered.txdb <- chrseparate(sample.Txdb,19)
trans.exon.range <- exonsBy(filtered.txdb,by="tx")
trans.intron.range <- intronsByTranscript(filtered.txdb)
txTable <- select(filtered.txdb, keys=names(trans.exon.range),
columns=c("TXID","TXNAME","GENEID","TXSTART","TXEND"), keytype="TXID")
ch.snp.locus <- as.matrix(samplesnplocus[samplesnplocus[,2] == 19,])
ch.snps <- matrix(ch.snp.locus[is.element(ch.snp.locus[,1],rownames(samplesnp)),],ncol=3,byrow=FALSE)
ch.snps.range <- GRanges(seqnames=Rle(19),ranges=IRanges(start=as.integer(ch.snps[,3]),
end=as.integer(ch.snps[,3])),metadata=ch.snps[,1])
Altvalue <- findAlternative("ENSG00000170889",txTable,trans.exon.range,trans.intron.range,19)
overlapsnp <- findOversnp(Altvalue,ch.snps.range)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(IVAS)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

No methods found in "BiocGenerics" for requests: unlist
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IVAS/findOversnp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findOversnp
> ### Title: Find SNPs which belongs to alternative exons and flanking
> ###   introns of them.
> ### Aliases: findOversnp
> 
> ### ** Examples
> 
> sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
> sample.Txdb <- loadDb(sampleDB)
> data(samplesnplocus)
> data(samplesnp)
> filtered.txdb <- chrseparate(sample.Txdb,19)
> trans.exon.range <- exonsBy(filtered.txdb,by="tx")
> trans.intron.range <- intronsByTranscript(filtered.txdb)
> txTable <- select(filtered.txdb, keys=names(trans.exon.range),
+ columns=c("TXID","TXNAME","GENEID","TXSTART","TXEND"), keytype="TXID")
'select()' returned 1:1 mapping between keys and columns
> ch.snp.locus <- as.matrix(samplesnplocus[samplesnplocus[,2] == 19,])
> ch.snps <- matrix(ch.snp.locus[is.element(ch.snp.locus[,1],rownames(samplesnp)),],ncol=3,byrow=FALSE)
> ch.snps.range <- GRanges(seqnames=Rle(19),ranges=IRanges(start=as.integer(ch.snps[,3]),
+ end=as.integer(ch.snps[,3])),metadata=ch.snps[,1])
> Altvalue <- findAlternative("ENSG00000170889",txTable,trans.exon.range,trans.intron.range,19)
> overlapsnp <- findOversnp(Altvalue,ch.snps.range)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>