View source: R/BiofeatureGraphics.R
imprintedGenes_GTEx | R Documentation |
Creates a track of imprinted genes from GTEx using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.
imprintedGenes_GTEx(gen="hg19", chr,start, end, tissues="all", classification="all",showId=FALSE, title="Imprinted genes GTEx")
gen |
the name of the genome. Default value=hg19 |
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) |
tissues |
list of tissues among 33 tissues in GTEx |
classification |
list of classification from 5 types (biallelic, consistent with biallelic, consistent with imprinting, imprinted, NC) |
showId |
logical. say if we write the name of group |
title |
The name of the annotation track |
An AnnotationTrack object of Gviz
Tiphaine Martin
http://bioconductor.org/packages/release/bioc/html/Gviz.html
Got to BindingMotifsBiomart binding motif biomart
library("Gviz") gen<-"hg19" chr<- "chr6" start <- 144251437 end <- 144330541 if(interactive()){ allIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, tissues="all", classification="imprinted",showId=TRUE) allimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, tissues="all", classification="imprinted",showId=TRUE) StomachIGtrack <-imprintedGenes_GTEx(gen,chr,start, end, tissues="Stomach", classification="all",showId=TRUE) PancreasIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, tissues="Pancreas", classification="all",showId=TRUE) PancreasimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, tissues="Pancreas", classification="biallelic",showId=TRUE) imprintinglist <- list(allIGtrack,allimprintedIGtrack, StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack) plotTracks(imprintinglist, from = start, to = end, fontfamily="sans",fontfamily.title="sans") } else { data(allIGtrack) data(allimprintedIGtrack) data(StomachIGtrack) data(PancreasIGtrack) data(PancreasimprintedIGtrack) imprintinglist <- list(allIGtrack,allimprintedIGtrack, StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack) plotTracks(imprintinglist, from = start, to = end, fontfamily="sans",fontfamily.title="sans") }
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