bsapply {BSgenome} | R Documentation

## bsapply

### Description

Apply a function to each chromosome in a genome.

### Usage

    bsapply(BSParams, ...)

### Arguments

`BSParams` | a BSParams object that holds the various parameters needed to configure the bsapply function
`...` | optional arguments to 'FUN'.

### Details

The `exclude` parameter of the `BSParams` object must be a character vector containing regular expressions. By default it's empty so nothing gets excluded. A popular option will probably be to set this to "rand" so that random bits of unassigned contigs are filtered out.

### Value

If `BSParams` sets `simplify=FALSE`, an ordinary list is returned containing the results generated using the remaining BSParams specifications. If `BSParams` sets `simplify=TRUE`, an `sapply`-like simplification is performed on the results.

### Author(s)

Marc Carlson

### See Also

BSParams-class, BSgenome-class, BSgenome-utils

### Examples

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

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

      ## Or we can do this same function with simplify = TRUE:
      params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
                                exclude = c("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.hg38.masked)
      genome <- BSgenome.Hsapiens.UCSC.hg38.masked
      ## 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 = genome, FUN = alphabetFrequency,
                                exclude = c(1:8,"M","X","_"), simplify = TRUE)
      bsapply(params)

      if (interactive()) {
        ## Set up the motifList to filter out all double T's and all double C's
        params@motifList <-c("TT","CC")
        bsapply(params)

        ## Get rid of the motifList
        params@motifList=as.character()
      }

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

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

      options(verbose=FALSE)

[Package BSgenome version 1.56.0 Index]