data:probeAnno          package:davidTiling          R Documentation

_A_n _e_n_v_i_r_o_n_m_e_n_t _w_i_t_h _p_r_o_b_e _m_a_p_p_i_n_g _i_n_f_o_r_m_a_t_i_o_n _f_o_r _t_h_e _S_c_e_r_e_v_i_s_i_a_e _t_i_l_i_n_g _a_r_r_a_y

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

     The environment contains probe mapping information for the
     Affymetrix Scerevisiaetiling chip from 2004, which was custom-made
     for the Stanford Genome Center. The chips tile the complete genome
     of S. cerevisiae in steps of 8 bases, separately for each strand
     of each chromosome. The two tiles for one chromosome (Watson and
     Crick strands) are offset by 4 bases.

     In the following a brief description of the 138 elements of the
     'probeAnno' environment.

     'probeReverse': a list of 8 factors, each of length 6553600,
     corresponding to the rows of 'davidTiling'. For example, if the
     probe corresponding to the j-th row in 'davidTiling' maps to the
     coding sequence of a gene, then the factor level of
     'probeRevers$CDS[j]' is the name of the gene, and the empty string
     '""' otherwise. This applies to samples that were hybridized to
     the chip after a reverse transcription step.

     'probeDirect': analogous to 'probeReverse', but for samples that
     were hybridized to the chip without a reverse transcription step.
     The probes map to the opposite chromosomal strand compared to
     experiments with  reverse transcription.

     '1.+.index': indices (from 1...6553600, corresponding to the rows
     of 'davidTiling') of probes mapping to the Watson strand of
     chromosome 1.

     '1.+.start', '1.+.end': start and end positions in genomic
     coordinates of the alignments of the probes (in the same order as
     in '1.+.index') to the Watson strand of chromosome 1. For 25-mers,
     the values in '1.+.end' are those in '1.+.start' plus 24, but not
     all probes on the array are 25-mers.

     '1.-.unique': specificity of the probe:

     _0 has exactly one perfect match (PM) and no near-matches in the
          genome

     _1 has exactly one PM and some near-matches

     _2 has no PM but one or more near-matches

     _3 has multiple PMs in the genome .in -5

          '1.-.index', '1.-.start', '1.-.end', '1.-.unique': analogous
          to the above, but for the Crick strand of chromosome 1.
          '2.+.index', '2.+.start', '2.+.end', '2.-.unique': analogous
          to the above, but for the Watson strand of chromosome 2; and
          so forth. "Chromosome 17" is mitochondrial DNA.

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

     data("probeAnno")

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

     W. Huber huber@ebi.ac.uk

_S_o_u_r_c_e:

     Probe sequences were obtained from Affymetrix in a file called
     'S.cerevisiae_tiling.1lq'. The genomic sequences of the S.
     cerevisiae chromosomes were downloaded  from
     'ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/chromosomes/fasta'
     on 7 Aug 2005, 18:16 BST in 17 files 'chr01.fsa'-'chr16.fsa', and
     'chrmt.fsa'. The probe sequences were matched against the
     chromosomal sequencences with the program 'MUMmer', see the script
     'mapProbesToGenome.sh' (in the 'inst/scripts' directory of this
     package). 'MUMmer' results were parsed and processed into the
     'probeAnno' environment with the script 'makeProbeAnno.R' (in the
     'inst/scripts' directory of this package).

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

     data("probeAnno")
     ls(probeAnno)
     str(probeAnno$"1.+.start")

