Makesense            package:geneplotter            R Documentation

_P_r_o_d_u_c_e _S_m_o_o_t_h_e_d _S_e_n_s_e/_A_n_t_i-_s_e_n_s_e _F_o_r _A_l_l _C_h_r_o_m_o_s_o_m_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     'Makesense' takes either an 'ExpressionSet' object or a 'matrix'
     of gene expressions and will produce a smoothed positive and
     negative strands for all chromosomes.

_U_s_a_g_e:

     Makesense(expr, lib, ...)

_A_r_g_u_m_e_n_t_s:

    expr: Either an 'ExpressionSet' or a 'matrix' of  gene expressions
          with genes as rows and columns as samples.

     lib: The name of the Bioconductor annotation data package that
          will be used to provide mappings from probes to chromosomal
          locations, such as 'hgu95av2.db' or 'hgu133a.db'.  If 'expr'
          is an 'ExpressionSet', the argument defaults to the
          'annotation' slot of the 'ExpressionSet'.

     ...: Currently, the only optional argument is 'f', the smoother
          span to be passed to 'lowess'. Its value should be in the
          interval of (0,1). This gives the proportion of points in the
          plot which influence the smooth at each value. Larger values
          give more smoothness.  The default value for this argument is
          1/10.

_D_e_t_a_i_l_s:

     The 'expr' argument can either be of class 'ExpressionSet' or
     'matrix', where the latter represents the matrix of gene
     expressions.

     If the 'expr' argument is an 'ExpressionSet', the 'lib' argument
     will use the 'annotation' slot.  Users can override this behaviour
     and supply their own 'lib' argument if they wish.  If the
     'ExpressionSet' has no value associated with the 'annotation' slot
     (which should not happen, but is possible) then the user must
     supply the 'lib' argument manually or the function will throw an
     error.

_V_a_l_u_e:

     A list of 2 components: 

    ans2: a 'list', whose components correspond to samples  in the same
          order as appearing in the columns of  'expr'. Each component
          is also a 'list', named by chromosomes  "1"-"22", "X" and
          "Y". Each named component is again a 'list'  with two
          elements named "posS" and "negS", corresponding to the
          positive and negative strands of a chromosome, each of which
          is an object returned by 'lowess'.

     lib: A string giving the name of the annotation data package to
          use.  Optional if 'expr' is an 'ExpressionSet'.

_A_u_t_h_o_r(_s):

     Robert Gentleman and Xiaochun Li

_S_e_e _A_l_s_o:

     'plotChr'

_E_x_a_m_p_l_e_s:

       if (require("hgu133a.db")) {
         data(expressionSet133a)
         esetobj <- Makesense(exprs(expressionSet133a), "hgu133a")
         esetobj2 <- Makesense(expressionSet133a[1:200, ])
       }

