R2BASE                 package:SAGx                 R Documentation

_P_r_o_d_u_c_e_s _a _B_A_S_E _f_i_l_e

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

     The function produces a BASE file for import to Gene Data Viewer.

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

     R2BASE(context.data = clingen, sample.ids = AZID, expression.data = dats, 
     annotation = annots, out = "u:\\temp\\temp.base")

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

context.data: e.g. a clinical database

sample.ids: Sample Ids, that names the columns of the expression data.

expression.data: a matrix with the gene expression data, samples
          correspond to columns and probesets to rows. It is assumed
          that probeset identifiers are found in the first column.

annotation: annotations of the probesets, i.e. the rows in the
          expression.data. It is assumed that probeset identifiers are
          found in the first column.

     out: the output file including path

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

     The file produced complies with an old BASE format. However, none
     of these formats are documented , as far as I know. So,
     essentially this function defines a data format that can be read
     by e.g. Gene Data Viewer.

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

     Per Broberg

