mergeCIstates: merge ChromImpute chromatin states, or GWAS hit indicators,...
In gQTLBase: gQTLBase: infrastructure for eQTL, mQTL and similar studies

Description Usage Arguments Value Examples

merge ChromImpute chromatin states, or GWAS hit indicators, to a GRanges

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mergeCIstates(gr, ermaset=NULL, epig, genome = "hg19", importFull=FALSE, useErma = TRUE, stateGR=NULL)
mergeGWhits(gr, gwcat, use=c("both", "addr", "name")[1],
     grSnpField="SNP")

`gr`	a GRanges instance
`ermaset`	an instance of `ErmaSet-class`. if NULL, supply a GRanges as stateGR, with fields states and statecols
`gwcat`	an instance of `gwaswloc-class`, or any compliant GRanges instance – must have mcols field `SNPS` with snp identifier
`epig`	the standardized epigenome name of the epigenome to use
`genome`	a tag for genome build
`importFull`	logical, set to TRUE to acquire entire content (for LNG.FET, 800K ranges), to avoid contention for connections in parallel applications
`useErma`	logical – at the moment, must be TRUE; plan is to allow use of elements of AnnotationHub
`use`	character string selecting approach for linking loci in `gr` to those in `gwcat` – if `"both"`, coincidence in address or name are both checked and used; if `"addr"`, only address is checked, if `"name"`, only SNP name.
`grSnpField`	character string naming the field in mcols(gr) with SNP id
`stateGR`	a GRanges instance as imported from erma package or from AnnotationHub, with mcols field states denoting chromatin state and statecols the associated colors for rendering

for mergeCIstates, a GRanges instance with additional fields in mcols: fullStates, states, and statecols, denoting respectively the full annotation of ChromImpute for the inferred state, an abbreviated tag that collapses related states, and a color tag for rendering, that does not replicate the colors in the ChromImpute bed files. The states field is a factor with levels c("Het", "DNAse", "Enh", "Prom", "Quies", "ReprPC", "Tss", "Tx", "ZNF/Rp").

for mergeGWhits, a single mcols field is added, isGwasHit, that is 1 for coincident hit and 0 otherwise. Eventually phenotype information will be collected and added.

## Not run:   # needs to use updated gwascat
if (require(gwascat) && require(erma)) {
#
# demonstrate Tx state for exon starts
#
  gm = resize(genemodel("ORMDL3"),1)
  es = makeErmaSet()
  g1 = mergeCIstates(gm, es, "LNG.FET")
  g1
#
# set up for GWAS
#
  require(GenomeInfoDb)
  data(ebicat37)
  genome(ebicat37) = "hg19"
  seqlevelsStyle(ebicat37) = "UCSC"
  g1 = c(g1, g1[1])  # add a known hit
  start(g1[length(g1)]) = 38062196
  mergeGWhits(g1, ebicat37)
  }
 
## End(Not run)