processCGH              package:snapCGH              R Documentation

_P_r_o_c_e_s_s _d_a_t_a _i_n _a_n _M_A_L_i_s_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes object of class 'MAList' and it re-orderes and
     filters clones based on their mapping information and proportion
     missing. It also average duplicated clones and imputes missing
     values for clones that are still NA after the filetering step.

_U_s_a_g_e:

     processCGH(input, maxChromThreshold = 22, minChromThreshold
                      = 1, method.of.averaging = NULL, ID = "ID")

_A_r_g_u_m_e_n_t_s:

   input: Object of class 'MAList' or 'RGList'

maxChromThreshold: Chromosomes are ordered and numbered as usual,
          except for X and Y chromosome, which in for Homo sapiens
          genome have numbers 23 and 24 repsectivelly, in for Mus
          musculus 20 and 21, etc. Remove chromosomes from segmentation
          analysis which are greater than this value.

minChromThreshold: Chromosomes are ordered and numbered as usual,
          except for X and Y chromosome, which in for Homo sapiens
          genome have numbers 23 and 24 repsectivelly, in for Mus
          musculus 20 and 21, etc. Remove chromosomes from segmentation
          analysis which re lower than this value.

method.of.averaging: If left as the default no combining of replicate
          spots takes place.  Other wise this should specify a function
          which takes a vector of duplicates and combines them into a
          single value.

      ID: Name of column in 'RG\$genes' corresponding to the clone
          names. For most data the default will work, however for affy
          data the value for ID should be '"CloneName"'

_V_a_l_u_e:

     Object of class 'SegList'

_A_u_t_h_o_r(_s):

     Jane Fridlyand, Peter Dimitrov, John Marioni and Mike Smith

_S_e_e _A_l_s_o:

     'MAList'

