ragged41FP {TxRegInfra} | R Documentation |
ragged41FP: A RaggedExperiment instance with digital genomic footprints over the coding region of ORMDL3
ragged41FP
DataFrame
data(ragged41FP) ragged41FP dim(ca <- compactAssay(ragged41FP,3)) # stat dim(sparseAssay(ragged41FP,3)) # stat opar = par(no.readonly=TRUE) par(mar=c(4,11,4,3), bg='lightgray') image(ca, main='over ORMDL3', axes=FALSE) labs = gsub('_DS.*._hg19_FP', '', colnames(ragged41FP)) axis(2, at=seq(0,1,length=41), ylab='41 tissues', labels=labs, cex.axis=.6, las=2) mtext('positions on chr17 not to scale\n(red = lower FOS = stronger binding capacity', 1, line=1) ## Not run: # if (interactive()) { m1 = mongolite::mongo(url=URL_txregInAWS(), db='txregnet') cd = makeColData(url=URL_txregInAWS(), db='txregnet') rme1 = RaggedMongoExpt(m1, cd[which(cd$type=='FP'),]) BiocParallel::register(BiocParallel::SerialParam()) # necessary for mac? raggHHIP = sbov(rme1, GRanges('chr4', IRanges(145565173, 145605173))) ca = compactAssay(raggHHIP,3)[seq_len(200),] image(ca, main='over HHIP', axes=FALSE) labs = gsub('_DS.*._hg19_FP', '', colnames(ca)) axis(2, at=seq(0,1,length=ncol(ca)), ylab=paste(ncol(ca), 'tissues'), labels=labs, cex.axis=.6, las=2) mtext('positions on chr4 not to scale\n(red = lower FOS = stronger binding capacity', 1, line=1) # } ## End(Not run) par(opar)