peak                  package:Ringo                  R Documentation

_C_l_a_s_s _p_e_a_k - _A _l_i_s_t _h_o_l_d_i_n_g _C_h_I_P-_c_h_i_p _p_e_a_k _c_h_a_r_a_c_t_e_r_i_s_t_i_c_s

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

     An object of class 'peak' is a list holding characteristics of an
     enrichment peak from ChIP chip data. While this is only a S3
     rather than a formal 'S4' class (yet), the presence of certain
     list elements enables a standardized approach to working with
     enriched regions identified from ChIP-chip data. Note that the
     term "peak", while commonly used in ChIP-chip context, is slightly
     misleading and the term "ChIP-enriched region" would be more
     appropriate. Within such regions the actual signal could show two
     or more actual signal peaks or none at all (long plateau). For
     succinctness sake, we use the term "peak" for a ChIP-enriched
     region, though.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     _n_a_m_e required character vector of length 1 unequivocally
          describing the peak, e.g. "Suz12.Nudt2.upstream.peak"

     _c_h_r required character vector of length one, naming the chromosome
          of the peak, e.g. "9" 

     _s_t_a_r_t required integer of peak start position on the chromosome,
          e.g. 34318900 

     _e_n_d required integer of peak start position on the chromosome,
          e.g. 34320100 

     _c_e_l_l_T_y_p_e optional character vector describing the cell type the
          ChIP chip experiment has been done on, e.g. "human"

     _a_n_t_i_b_o_d_y required character vector describing the antibody or
          characteristic for which fragments were supposedly enriched
          in immuno-precipitation step, e.g. "Suz12" for the protein
          Suz12

     _t_y_p_e_U_p_s_t_r_e_a_m optional character vector of features that this peak
          is located upstream of, e.g. the transcriptional start site
          of "ENST00000379158". See 'relatePeaks' for details.

     _t_y_p_e_D_o_w_n_s_t_r_e_a_m optional character vector of features that this
          peak is located downstream of 

     _m_a_x_P_e_a_k optional numeric of maximal (smoothed) probe level in the
          peak, e.g. 2.00

     _s_c_o_r_e optional numeric of a peak score, currently we use the sum
          of smoothed probe levels (log fold changes), e.g. 69.16

     _p_r_o_b_e_s optional character vector of probe identifiers of all
          probes with match positions in the peak 

     _d_i_s_t_M_i_d_2_T_S_S optional named numeric vector of distances of the peak
          middle position to features, e.g. TSSs of transcripts up- and
          downstream; names are the features to which the distances are
          given; only meaningful in combination with 'typeUpstream' and
          'typeDownstram'; e.g. 55 with name "ENST00000379158"

     _u_p_S_y_m_b_o_l optional character vector of gene symbols of features the
          peak is located upstream of; supplements 'typeUpstream'; e.g.
          "Nudt2" 

     _d_o_w_n_S_y_m_b_o_l optional character vector of gene symbols of features
          the peak is located upstream of; supplements
          'typeDownstream'.

     ... further list elements can be added like normal list elements.

_C_r_e_a_t_i_o_n:

     Objects of class 'peak' are created by other functions, such as
     'findPeaksOnSmoothed'; or by creating a list with the respective
     components and assigning it the class 'peak', which is
     essentially, what the function 'newPeak' does.

_M_e_t_h_o_d_s:

     Methods defined for lists of class 'peak' are 'print.peak' and
     'plot.peak'.

_p_e_a_k_L_i_s_t:

     A list in which each element is of class 'peak', is called a
     'peakList'. This class, however, is not much in use yet.

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

     Joern Toedling, Tammo Krueger, PT Bote

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

     'plot.peak', 'findPeaksOnSmoothed', 'relatePeaks'

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

       exDir <- system.file("exData",package="Ringo")
       load(file.path(exDir,"exampleProbeAnno.rda"))
       load(file.path(exDir,"exampleX.rda"))
       smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
        modColumn = "Cy5", allChr = "9", winHalfSize = 400)
       peaksX <- findPeaksOnSmoothed(smoothX, probeAnno=exProbeAnno,
        thresholds=0.45, allChr="9", distCutOff=600)
       peaksX <- relatePeaks(peaksX, exGFF)
       str(peaksX[[1]])

