ragged41FP: ragged41FP: A RaggedExperiment instance with digital genomic...

In TxRegInfra: Metadata management for multiomic specification of transcriptional regulatory networks

Description

ragged41FP: A RaggedExperiment instance with digital genomic footprints over the coding region of ORMDL3

Usage

ragged41FP

Format

DataFrame

Note

The text on plot refers to FOS = 'footprint occupancy score' as in Neph et al, Nature 489, 6 Sept 2012 p 84.

Examples

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)

TxRegInfra documentation built on Nov. 8, 2020, 5:15 p.m.