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Last data update: 2014.03.03

R: Find SQTLs.

sqtlfinder

R Documentation

Find SQTLs.

Description

Find significant SNPs using the calSignificant function.

Usage

sqtlfinder(altInvalue = NULL, overapvalue = NULL, expdata = NULL, snpdata = NULL, method = NULL)

Arguments

`altInvalue`	A list data set from the findAlternative function.
`overapvalue`	A matrix data with SNPs in the flanking introns of alternative exons and ranges of those SNPs from findOversnp function.
`expdata`	Expression data of samples.
`snpdata`	Genotype data of samples.
`method`	The option for statistical models and boxplot.("lm" : analysis using linear regression model, "glm" : analysis using generalized linear mixed model, "both" : "lm" and "glm",and "boxplot" : for writing boxplot).

Value

The lm or glm method returns matrix data including SNP markers ID, chromosome number, alternative exons range, intron ranges, alternative type, P value, information of differential median values of expression ratio among genotypes ("sig" if differential median > 0.1 and "not sig" otherwise), a gene name, methods ("lm" or "glm"),and strand information of the gene. The boxplot method returns matrix data with relative ratio values and genotypes of samples.

Author(s)

Seonggyun Han, Sangsoo Kim

Examples

sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
sample.Txdb <- loadDb(sampleDB)
data(samplesnplocus)
data(sampleexp)
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)
sqtl.result <- sqtlfinder(Altvalue,overlapsnp,sampleexp,samplesnp,"lm")

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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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/sqtlfinder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sqtlfinder
> ### Title: Find SQTLs.
> ### Aliases: sqtlfinder
> 
> ### ** Examples
> 
> sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
> sample.Txdb <- loadDb(sampleDB)
> data(samplesnplocus)
> data(sampleexp)
> 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)
> sqtl.result <- sqtlfinder(Altvalue,overlapsnp,sampleexp,samplesnp,"lm")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>