DNAse_UCSC {coMET} | R Documentation |
Creation of DNase cluster track from a connection to UCSC genome browser in using the GViz bioconductor package
DNAse_UCSC(gen, chr, start, end, mySession, title="DNA cluster", track.name = "DNase Clusters", table.name = NULL)
gen |
the name of the genome. Data is not currently available for GRCh38 (hg38). |
chr |
the chromosome of interest |
start |
the first position in the region of interest (the smallest value) |
end |
the last position in the region of interest (the largest value) |
mySession |
the object session from the function browserSession of rtracklayer |
title |
Name of tracks |
track.name |
the name of the track DNAse_UCSC. "DNase Clusters"(default) |
table.name |
the name of the table from the track |
An AnnotationTrack object of Gviz
Tiphaine Martin
http://bioconductor.org/packages/release/bioc/html/Gviz.html
http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeDNAseSuper
library("Gviz") library("rtracklayer") gen <- "hg19" chr <- "chr7" start <- 38290160 end <- 38303219 if(interactive()){ BROWSER.SESSION="UCSC" mySession <- browserSession(BROWSER.SESSION) genome(mySession) <- gen track.name="Broad ChromHMM" tablestrack<-tableNames(ucscTableQuery(mySession, track=track.name)) table.name<-tablestrack[1] dnasetrack<-DNAse_UCSC(gen,chr,start,end,mySession) plotTracks(dnasetrack, from = start, to =end) }else { data(dnasetrack) plotTracks(dnasetrack, from = start, to =end) }