\name{bsapply}

\alias{bsapply}

\title{bsapply}

\description{
  Apply a function to each chromosome in a genome.
}

\usage{
  bsapply(BSParams, ...)
}

\arguments{
  \item{BSParams}{
    a BSParams object that holds the various parameters needed to
    configure the bsapply function
  }
  \item{...}{
    optional arguments to 'FUN'.
  }
}

\details{
  By default the exclude parameter is set to not exclude anything.  A
  popular option will probably be to set this to "rand" so that random
  bits of unassigned contigs are filtered out.
}

\value{
  A named list is returned where each element is whatever was returned by the
  function FUN.  The names of the list correspond to the names of the
  chromosomes as they were labeled by the BSgenome obect in the slot
  accessed by seqnames().
}

\author{Marc Carlson}

\seealso{
  \link{BSgenome-class}
}

\examples{
  ## Load the Worm genome:
  library("BSgenome.Celegans.UCSC.ce2")

  ## Count the alphabet frequencies for every chromosome but exclude
  ## mitochrondrial ones:
  params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
  exclude = "M")
  bsapply(params)

  ## Or we can do this same function with the simplif option:
  params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
  exclude = "M", simplify = TRUE)
  bsapply(params)


  ## Examples to show how we might look for a string (in this case an
  ## ebox motif) across the whole genome.  
  Ebox <- DNAStringSet("CACGTG")
  pdict0 <- PDict(Ebox)

  params <- new("BSParams", X = Celegans, FUN = countPDict, simplify = TRUE)
  bsapply(params, pdict = pdict0)

  params@FUN <- matchPDict
  bsapply(params, pdict = pdict0)

  ## And since its really overkill to use matchPDict to find a single pattern:
  params@FUN <- matchPattern
  bsapply(params, pattern = "CACGTG")


  ## Examples on how to use the masks
  library("BSgenome.Hsapiens.UCSC.hg18")
  ## I can make things verbose if I want to see the chromosomes getting processed.
  options(verbose=TRUE)
  ## For the 1st example, lets use default masks
  params <- new("BSParams", X = Hsapiens, FUN = alphabetFrequency,
  exclude = c(1:8,"random","hap"), simplify = TRUE)
  bsapply(params)

  ##Enable all masks
  params@maskList <- c("RM"=TRUE,"TRF"=TRUE)
  bsapply(params)

  ##Disable all masks
  params@maskList <- c("AGAPS"=FALSE,"AMB"=FALSE)
  bsapply(params)

}

\keyword{manip}