Amellifera package:BSgenome.Amellifera.UCSC.apiMel2 R Documentation

_A_p_i_s _m_e_l_l_i_f_e_r_a (_H_o_n_e_y _B_e_e) _f_u_l_l _g_e_n_o_m_e (_U_C_S_C _v_e_r_s_i_o_n _a_p_i_M_e_l_2)

_D_e_s_c_r_i_p_t_i_o_n:

     Apis mellifera (Honey Bee) full genome as provided by UCSC
     (apiMel2, Jan. 2005) and stored in Biostrings objects.

_N_o_t_e:

     This BSgenome data package was made from the following source data
     files:


     sequences:
     http://hgdownload.cse.ucsc.edu/goldenPath/apiMel2/bigZips/GroupFa.zip
     AGAPS masks:
     http://hgdownload.cse.ucsc.edu/goldenPath/apiMel2/database/gap.txt.gz
     RM masks:
     http://hgdownload.cse.ucsc.edu/goldenPath/apiMel2/bigZips/GroupOut.zip

     See '?BSgenomeForge' and the BSgenomeForge vignette
     ('vignette("BSgenomeForge")') in the BSgenome software package for
     how to make a BSgenome data package.

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

     BSgenome-class, DNAString-class, 'available.genomes',
     BSgenomeForge

_E_x_a_m_p_l_e_s:

     Amellifera
     seqlengths(Amellifera)
     Amellifera$Group1  # same as Amellifera[["Group1"]]

     if ("AGAPS" %in% masknames(Amellifera)) {

       ## Check that the assembly gaps contain only Ns:
       checkOnlyNsInGaps <- function(seq)
       {
         ## Replace all masks by the inverted AGAPS mask
         masks(seq) <- gaps(masks(seq)["AGAPS"])
         af <- alphabetFrequency(seq)
         found_letters <- names(af)[af != 0]
         if (any(found_letters != "N"))
             stop("assembly gaps contain more than just Ns")
       }

       ## A message will be printed each time a sequence is removed
       ## from the cache:
       options(verbose=TRUE)

       for (seqname in seqnames(Amellifera)) {
         cat("Checking sequence", seqname, "... ")
         seq <- Amellifera[[seqname]]
         checkOnlyNsInGaps(seq)
         cat("OK\n")
       }
     }

     ## See the GenomeSearching vignette in the BSgenome software
     ## package for some examples of genome-wide motif searching using
     ## Biostrings and the BSgenome data packages:
     if (interactive())
         vignette("GenomeSearching", package="BSgenome")

