crlmm                 package:oligo                 R Documentation

_G_e_n_o_t_y_p_e _C_a_l_l_s

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

     Performs genotype calls via CRLMM (Corrected Robust Linear Model
     with Maximum-likelihood based distances).

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

     crlmm(object, correction = NULL, recalibrate = TRUE, minLLRforCalls =
     c(5, 1, 5), verbose = TRUE,  correctionFile = NULL, prefix =
     "tmp.crlmm.", balance = 1.5)
     justCRLMM(filenames, batch_size = 40000, minLLRforCalls = c(5, 1, 5),
     recalibrate = TRUE, balance = 1.5, phenoData = NULL, verbose = TRUE,
     pkgname = NULL)

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

  object: 'SnpQSet' object

filenames: character vector with the filenames.

batch_size: integer defining how many SNPs should be processed at a
          time.

correction: The output of the EM algorithm

recalibrate: Logical - should recalibration be performed?

  prefix: String defining the prefix to be used with the temporary
          files.

 balance: Control parameter to balance homozygotes and heterozygotes
          calls.

minLLRforCalls: Minimum thresholds for genotype calls.

 verbose: Logical.

correctionFile: A filename.

phenoData: 'phenoData' object or 'NULL'

 pkgname: alt. pdInfo package to be used

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

     The 'correctionFile' is a string (eg, "outputEM.rda") pointing to
     a filename. If the file does not exist, 'crlmm' will save a file
     with that name containing the results of the EM algorithm. If the
     file exists, its content is loaded and used by CRLMM. The
     'correctionFile' is meant to save time if 'crlmm' is be run
     multiple times, as the EM algorithm does not need to be run
     everytime.

     The 'justCRLMM' method is more efficient in terms of memory. It
     uses the CEL files directly, taking SNPs by batch.

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

     'SnpCallSetPlus' object.

_N_o_t_e:

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

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

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

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

     ## crlmmResults <- justCRLMM(list.celfiles())

