bb_params: BentoBox parameters object

Creates an object of class "bb_params" that can be used by BentoBox functions. bb_params can be used to set a set of parameters to be shared across multiple functions.

bb_params(
  BSgenome = NULL,
  OrgDb = NULL,
  TxDb = NULL,
  alpha = NULL,
  altchrom = NULL,
  altchromend = NULL,
  altchromstart = NULL,
  althalf = NULL,
  apa = NULL,
  arch = NULL,
  archHeight = NULL,
  assembly = "hg19",
  at = NULL,
  bed = NULL,
  bedpe = NULL,
  bg = NULL,
  binCap = NULL,
  binSize = NULL,
  border = NULL,
  boxHeight = NULL,
  boxWidth = NULL,
  buffer = NULL,
  cex = NULL,
  check.overlap = NULL,
  chrom = NULL,
  chromend = NULL,
  chromstart = NULL,
  col = NULL,
  colorby = NULL,
  colorbyStrand = NULL,
  colorbyrange = NULL,
  commas = NULL,
  cutoffArches = NULL,
  dataType = NULL,
  decreasing = NULL,
  default.units = NULL,
  display.column = NULL,
  draw = NULL,
  end = NULL,
  equalLengthOut = NULL,
  filename = NULL,
  fill = NULL,
  fillcolor = NULL,
  fontcolor = NULL,
  fontcolors = NULL,
  fontsize = NULL,
  gene = NULL,
  gene.id.column = NULL,
  geneBackground = NULL,
  geneBuffer = NULL,
  geneHighlights = NULL,
  geneOrder = NULL,
  genome = NULL,
  gp = NULL,
  half = NULL,
  height = NULL,
  hic = NULL,
  hicFile = NULL,
  highlightCol = NULL,
  interactions = NULL,
  just = NULL,
  label = NULL,
  labels = NULL,
  legend = NULL,
  linecolor = NULL,
  loops = NULL,
  lty = NULL,
  lwd = NULL,
  main = NULL,
  n = NULL,
  norm = NULL,
  orientation = NULL,
  pVals = NULL,
  palette = NULL,
  pch = NULL,
  plot = NULL,
  position = NULL,
  r = NULL,
  range = NULL,
  res = NULL,
  res_scale = NULL,
  resolution = NULL,
  rot = NULL,
  scale = NULL,
  sequence = NULL,
  shift = NULL,
  showOutline = NULL,
  showRuler = NULL,
  showUnit = NULL,
  sigCol = NULL,
  sigLine = NULL,
  sigVal = NULL,
  signal = NULL,
  space = NULL,
  spaceHeight = NULL,
  spaceWidth = NULL,
  start = NULL,
  strand = NULL,
  strandLabels = NULL,
  strandSplit = NULL,
  strandcolors = NULL,
  stroke = NULL,
  style = NULL,
  tcl = NULL,
  ticks = NULL,
  title = NULL,
  type = NULL,
  width = NULL,
  x = NULL,
  xgrid = NULL,
  y = NULL,
  ygrid = NULL,
  ymax = NULL,
  zrange = NULL
)

Arguments

assembly	string defining the genome build. Default value is assembly = "hg19".
gene	(optional) string naming a gene used to set the chromosome, chromstart, and chromend arguments.
geneBuffer	(optional) integer base-pairs to extend the start and end of a gene defined by argument gene.
...	This function will take any BentoBox function parameters and their values.

Value

Returns an object of class "bb_params" containing BentoBox function arguments.

Details

bb_params generates arguments from exported BentoBox functions at loading time of the package. Arguments defined in a bb_params object can be passed into the params argument of BentoBox functions. bb_params arguments can be overridden from within BentoBox functions.

bb_params also provides an alternative region definition mechanism. Given a gene name and genome assembly, bb_params returns the appropriate "chrom", "chromstart", and "chromend" with a default buffer of (gene length) / 2 added to the ends of the gene coordinates. The buffer amount can be set manually with the geneBuffer parameter. Buffer extending beyond the length of the chromosome will be trimmed.

Examples

## Define parameters
p1 <- bb_params(gene = "IL1B", assembly = "hg19")

## Optionally add more parameters
p2 <- bb_params(geneBuffer = 10000)

## Combine parameters and pass them to a BentoBox function
bb_plotGenes(params = c(p1, p2))