convertSmc               package:PGSEA               R Documentation

_C_o_n_v_e_r_t _E_n_t_r_e_z _I_D _b_a_s_e_d "_s_m_c" _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function will convert the Entrez IDs of an smc object to the
     corresponding Entrez IDs from a different species. Data from the
     homologene project is downloaded and used within this function.

_U_s_a_g_e:

     convertSmc(mcs, fromSpecies = "h", toSpecies = "r",hgX="./homologene.data")

_A_r_g_u_m_e_n_t_s:

     mcs: a list of "smc" objects

fromSpecies: character - a single letter describing the species to
          convert from ie, h=human, r= rat, etc..

toSpecies: character - a single letter describing the species to
          convert to ie, h=human, r= rat, etc.. 

     hgX: character - file name of homologene data file 

_D_e_t_a_i_l_s:

     This function will not work if you have not downloaded the
     homologene data file. Please use this command to do so:
     download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")

_V_a_l_u_e:

     a list of converted "smc" objects

_A_u_t_h_o_r(_s):

     Karl Dykema <karl.dykema@vai.org>

_E_x_a_m_p_l_e_s:

     ## Not run: 
             download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")
             
             datadir <- system.file("data", package = "PGSEA")
             sample <- readGmt(file.path(datadir, "sample.gmt"))
             
             converted <- convertSmc(sample[1:2],"h","r")
             str(converted)
     ## End(Not run)

