cher-class               package:Ringo               R Documentation

_C_l_a_s_s "_c_h_e_r" - _C_h_I_P-_e_n_r_i_c_h_e_d _r_e_g_i_o_n

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

     An object of class 'cher' (ChIP-enriched region) holds
     characteristics of an enriched genomic region from ChIP chip data.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("cher", name,
     chromosome, start, end, cellType, antibody, maxLevel, score,
     probes, extras, ...)'.

_S_l_o_t_s:


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

     '_c_h_r_o_m_o_s_o_m_e': character vector of length one, naming the
          chromosome of the region, e.g. "9"

     '_s_t_a_r_t': 'integer', region start position on the chromosome, e.g.
          34318900 

     '_e_n_d': 'integer', region end position on the chromosome, e.g.
          34320100

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

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

     '_m_a_x_L_e_v_e_l': 'numeric', maximal (smoothed) probe level in the cher,
          e.g. 2.00

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

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

     '_e_x_t_r_a_s': 'list' of further elements used to annotate the 'cher';
          examples of such that are used in 'Ringo' are:

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

          _t_y_p_e_I_n_s_i_d_e optional character vector of features that this
               'cher' is located inside of 

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

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

          _i_n_S_y_m_b_o_l optional character vector of gene symbols of
               features the cher is located upstream of; supplements
               'typeInside'.

          ... further list elements can be added using the 'update'
               method.


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


     _i_n_i_t_i_a_l_i_z_e create a new 'cher'; see section 'examples' below

     _p_l_o_t calls 'chipAlongChrom' to plot the 'cher'; see 'plot.cher'
          for more details

     _u_p_d_a_t_e signature('cher',...); updates elements of the 'cher'
          object; The further arguments in '...' are interpreted.
          Arguments corresponding to defined slot names of the 'cher'
          result in the value by that slot being replaced by the
          specified value for the argument; argument names that do not
          correspond to slot names of the object result in list
          elements of the 'extras' list of the 'cher' being replaced by
          the given values for these arguments or the values are
          appended to the current 'extras' list and the argument names
          make up the list names of the appended arguments. See section
          'examples' below for an example how to use this method.

     _c_e_l_l_T_y_p_e obtain or replace the description of the cell type, the
          ChIP-enriched regions was found in with this antibody

_c_h_e_r_L_i_s_t:

     A list in which each element is of class 'cher', is called a
     'cherList'. This class, however, is rarely used (yet).

_N_o_t_e:

     The 'cher' class used to be an S3 list before.

     The term 'cher' is shorthand for 'ChIP-enriched region'. We think
     this term is more appropriate than the term 'peak' commonly used
     in ChIP-chip context. Within such regions the actual signal could
     show two or more actual signal peaks or none at all (long
     plateau).

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

     Joern Toedling, Tammo Krueger

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

     'plot.cher', 'findChersOnSmoothed', 'relateChers'

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

       ## how to create a cher object from scratch
       cherNudt2 <- new("cher", name="nudt2.cher", chromosome=9,
                        start=34318954, end=34319944, antibody="Suz12",
                        maxLevel=2.00, score=69.2, upSymbol="NUDT2")
                        #extras=list(upSymbol="NUDT2"))
       cherNudt2
       str(cherNudt2)

       ## use the update method (note:this update is biologically meaningless)
       cher2 <- update(cherNudt2, cellType="HeLa", downSymbol="P53",
                       probes=c("probe1","probe2"))
       cher2; str(cher2)

       ## plot a cher object
       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)
       plot(cherNudt2, smoothX, probeAnno=exProbeAnno, gff=exGFF, extent=5000)

