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 not a formal
     'S4' class (yet), the presence of certain list elements enables a
     standardized approach to working with peaks identified from the
     data.

_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.  'H3ac.chr8.peak1' 

     _c_h_r required character vector of length one, naming the chromosome
          of the peak, e.g. "8" 

     _s_t_a_r_t required integer of peak start position on the chromosome,
          e.g. 60209200 

     _e_n_d required integer of peak start position on the chromosome,
          e.g. 60209540 

     _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. "cellLine.HL1"

     _m_o_d_i_f_i_c_a_t_i_o_n required character vector describing the modification
          or characteristic for which fragments were supposedly
          enriched in immuno-precipitation step, e.g. "H3ac" for
          acetylation of histone 3

     _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 "ENSMUST00000040104". 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. 1.74 

     _s_c_o_r_e optional numeric of a peak score, currently we use the sum
          of smooted probe levels (log fold changes), e.g. 0.703 

     _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. 1502 with name "ENSMUST00000040104"

     _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.
          "Hand2" 

     _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):

     Tammo Krueger, Joern Toedling

_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 = c("8"), winHalfSize = 400,
          combineReplicates = TRUE)
       peaksX <- findPeaksOnSmoothed(smoothX, probeAnno=exProbeAnno,
     thresholds=1.5, allChr = c("8"),distCutOff=600)
       peaksX <- relatePeaks(peaksX, exGFF)
       str(peaksX[[2]])

