R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Find SQTLs in multiple genes.

MsqtlFinder

R Documentation

Find SQTLs in multiple genes.

Description

This function enables one to analyze multiple genes using multi-thread version of the foreach function and joins output results from sqtlfinder function. Moreover, it calculates the FDR using P-values of the matrix result data.

Usage

MsqtlFinder(expdata = NULL, snpdata = NULL, snplocus = NULL, GTFdata = NULL,
met = NULL, Ncor = 1, bplotout = NULL, cutFDR = 0.01)

Arguments

`expdata`	Dataframe of expression data.
`snpdata`	Dataframe of genotype data.
`snplocus`	Locus of SNP markers in the snpdata.
`GTFdata`	The transcriptDb object in the GnomicFeatures package.
`met`	The option for statistical models.("lm" : analysis using linear regression model, "glm" : analysis using generalized linear mixed model,and "both" : "lm" and "glm").
`Ncor`	The number of cores for multi-threads.
`bplotout`	A directory saving boxplots
`cutFDR`	The false discovery rate value you would like to set threshold.

Value

This function returns the result matrix 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), gene names, methods ("lm" or "glm").

Author(s)

Seonggyun Han, Sangsoo Kim

References

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Morgan M, and Carey V. Software for Computing and Annotating Genomic Ranges. PLoS Computational Biology, 9, e1003118. 2013.

Benjamini, Yoav, Hochberg, and Yosef. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57, 289-300. 1995.

Examples

sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
sample.Txdb <- loadDb(sampleDB)
data(sampleexp)
data(samplesnp)
data(samplesnplocus)
#final.result <- MsqtlFinder(sampleexp,samplesnp,samplesnplocus,sample.Txdb,"lm",1)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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/MsqtlFinder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MsqtlFinder
> ### Title: Find SQTLs in multiple genes.
> ### Aliases: MsqtlFinder
> 
> ### ** Examples
> 
> sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
> sample.Txdb <- loadDb(sampleDB)
> data(sampleexp)
> data(samplesnp)
> data(samplesnplocus)
> #final.result <- MsqtlFinder(sampleexp,samplesnp,samplesnplocus,sample.Txdb,"lm",1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>