bsapply               package:BSgenome               R Documentation

_b_s_a_p_p_l_y

_D_e_s_c_r_i_p_t_i_o_n:

     Apply a function to each chromosome in a genome.

_U_s_a_g_e:

       bsapply(BSParams, ...)

_A_r_g_u_m_e_n_t_s:

BSParams: a BSParams object that holds the various parameters needed to
          configure the bsapply function 

     ...: optional arguments to 'FUN'. 

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

     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().

_A_u_t_h_o_r(_s):

     Marc Carlson

_S_e_e _A_l_s_o:

     BSgenome-class

_E_x_a_m_p_l_e_s:

       ## 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)

