Athaliana  package:BSgenome.Athaliana.TAIR.01222004  R Documentation

_A_r_a_b_i_d_o_p_s_i_s _t_h_a_l_i_a_n_a _f_u_l_l _g_e_n_o_m_e (_T_A_I_R _v_e_r_s_i_o_n _f_r_o_m _J_a_n_u_a_r_y _2_2, _2_0_0_4)

_D_e_s_c_r_i_p_t_i_o_n:

     Arabidopsis thaliana full genome as provided by TAIR (snapshot
     from January 22, 2004) and stored in Biostrings objects.

_N_o_t_e:

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


     ATH1_chr1.1con.01222004
     ATH1_chr2.1con.01222004
     ATH1_chr3.1con.01222004
     ATH1_chr4.1con.01222004
     ATH1_chr5.1con.01222004
     mitochondrial_genomic_sequence
     ATH1_chloroplast.1con.01072002
     from
     ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/OLD/

     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:

     Athaliana
     seqlengths(Athaliana)
     Athaliana$chr1  # same as Athaliana[["chr1"]]

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

       ## 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(Athaliana)) {
         cat("Checking sequence", seqname, "... ")
         seq <- Athaliana[[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")

