genes1d                package:made4                R Documentation

_g_e_n_e_s_1_d: _l_i_s_t _t_o_p _N _v_a_r_i_a_b_l_e_s _o_n _o_n_e _a_x_i_s. _L_i_s_t_s _t_h_e _m_a_x_i_m_u_m _a_n_d _m_i_n_i_m_u_m 
_v_a_l_u_e_s _i_n _a _c_o_l_u_m_n _o_f _a _d_a_t_a._f_r_a_m_e

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

     Lists the top N variables from the positive and negative ends of
     an axis. Returns a list of N variables that have the max and min.
     Given a $co or $li file it will return that variables at the ends
     of the axis.

_U_s_a_g_e:

     genes1d(array, n = 5, axis = 1, listgenes = FALSE)

_A_r_g_u_m_e_n_t_s:

   array: A 'matrix' or 'data.frame'. Typically a $co or $li from 
          'bga', 'cia' or  'dudi'.

       n: An integer indicating the number of variables to be returned.
          Default is 5. 

    axis: An integer indicating the column of x. Default is 1 (first
          axis, of $co or $li file) 

listgenes: A logical, If TRUE a list containing the variables  at each
          ends of the axes are returned

     ...: further arguments passed to or from other methods 

_D_e_t_a_i_l_s:

     Genes1d is similar to 'link[made4:genes]{genes}', but returns  an
     index of genes at the ends of one axes.

_V_a_l_u_e:

     Returns a vector or list of vectors.

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

     Aedin Culhane

_R_e_f_e_r_e_n_c_e_s:

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

     See Also as 'genes'

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

     data(khan)
     if (require(ade4, quiet = TRUE)) {
     khan.coa<-dudi.coa(khan$train[1:100,1:10], scannf=FALSE, nf=2)
     }
     ind<-topgenes(khan.coa$li, ends="pos")
     ind.ID<-topgenes(khan.coa$li, ends="pos", labels=khan$gene.labels.imagesID)
     ind.symbol<-topgenes(khan.coa$li, ends="pos", labels=khan$annotation$Symbol)
     Top10.pos<- cbind("Gene Symbol"=ind.symbol, 
     "Clone ID"=ind.ID, "Coordinates"=khan.coa$li[ind,], row.names=c(1:length(ind)))
     Top10.pos

