coMET (version 1.4.4)

eQTL: Creates a track from a file for eQTL data

Description

Creates a track from a BED file for eQTL data using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

eQTL(gen,chr, start, end, bedFilePath, featureDisplay, showId=FALSE,type_stacking="squish",just_group="above" )

Arguments

gen

the name of the genome.

chr

The chromosome of interest

start

The starting position in the region of interest (the smallest value)

end

The end position in the region of interest (the largest value)

bedFilePath

The file path to the .BED file containing the data to be visualised

featureDisplay

A vector of eQTL features to be displayed, such as SNP. Spelling and capitalisation of features must be identical to those in the user guide. There are three possibilities. First, the visualisation of only one feature (e.g. featureDisplay <- "CpG"), only the name of the specific feature is required. Second, visualisation of a set of features, for this a vector of features is required (e.g. featureDisplay <- c("SNP","CpG")). Finally, visualison all features in the genomic region, achived by using the word "all" (e.g. featureDisplay <- "all"), "all" is set by default. You can find the complete list of features and their associated colours in the user guide.

showId

Allows to visualise the Id of eQTL group.

type_stacking

Object of class"character", the stacking type of overlapping items on the final plot.One in c(hide, dense, squish, pack,full). More information cf the option "stacking" in Gviz

just_group

position. say where we write the name of group (choice in c("above","righ","left"))

Value

An AnnotationTrack object of Gviz

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- "SNP"
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "eQTL.bed")

if(interactive()){
  eQTLTrackSingle <- eQTL(gen,chr,start, end, bedFilePath, featureDisplay = featureDisplay )
  plotTracks(eQTLTrackSingle, from = start, to = end)
} else {
  data(eQTLTrackSingle)
  plotTracks(eQTLTrackSingle, from = start, to = end)
}

###########

library("Gviz")
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- c("SNP","mRNA_pheno")
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "eQTL.bed")

if(interactive()){
  eQTLTrackMultiple <- eQTL(gen,chr,start, end, bedFilePath, featureDisplay = featureDisplay )
  plotTracks(eQTLTrackMultiple, from = start, to = end)
} else {
  data(eQTLTrackMultiple)
  plotTracks(eQTLTrackMultiple, from = start, to = end)
}

######

library("Gviz")
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- "all"
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "eQTL.bed")

if(interactive()){
  eQTLTrackAll <- eQTL(gen,chr,start, end, bedFilePath, featureDisplay = featureDisplay )
  plotTracks(eQTLTrackAll, from = start, to = end)
} else {
  data(eQTLTrackAll)
  plotTracks(eQTLTrackAll, from = start, to = end)
}