viewByGene: multimodal Gviz-based visualization of MOWChIP tracks

In vjcitn/mowChIP: Infrastructure for microfluidic oscillatory washing-based ChIP

Description

multimodal Gviz-based visualization of MOWChIP tracks

Usage

viewByGene(gf = caoChIP[, 1:6], sym = "IGHA2", radius = 1e+05, gstr,
  namegen = function(x) x$numCells[1], ...)

Arguments

gf	GenomicFiles instance giving paths to .bw files
sym	gene symbol
radius	number of bp around coding region to display
gstr	a GRanges with gene annotation information, e.g., genes(EnsDb.Hsapiens.v75)
namegen	a function of one argument assumed to be a row of colData(gf) that will be used as the name parameter for the DataTrack derived from each sample
...	passed to plotTracks exclusive of type which is set to "polygon"

Examples

data(caoChIP)
S3paths = mowChInS3()
if (interactive()) {
 remoteMowK4me3 = GenomicFiles(files=S3paths[1:4], 
    colData=colData(caoChIP[,c(1,3,5,7)]))
 remoteMowK27ac = GenomicFiles(files=S3paths[5:8], 
    colData=colData(caoChIP[,c(9,11,13,15)]))
 require(EnsDb.Hsapiens.v75)
 gg = genes(EnsDb.Hsapiens.v75)
 require(GenomeInfoDb)
 seqlevelsStyle(gg) = "UCSC"
 viewByGene(gf=remoteMowK4me3, sym="IGHA2", radius=80000, gstr=gg)
 viewByGene(gf=remoteMowK27ac, sym="SPI1", radius=80000, gstr=gg)
 }

vjcitn/mowChIP documentation built on May 8, 2019, 2:34 a.m.