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(filenames, outdir, batch_size=40000, balance=1.5,
           minLLRforCalls=c(5, 1, 5), recalibrate=TRUE,
           verbose=TRUE, pkgname, reference=TRUE)
     justCRLMM(filenames, batch_size = 40000, minLLRforCalls = c(5, 1, 5),
     recalibrate = TRUE, balance = 1.5, phenoData = NULL, verbose = TRUE,
     pkgname = NULL, tmpdir=tempdir())

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

filenames: character vector with the filenames.

  outdir: directory where the output (and some tmp files) files will be
          saved.

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

recalibrate: Logical - should recalibration be performed?

 balance: Control parameter to balance homozygotes and heterozygotes
          calls.

minLLRforCalls: Minimum thresholds for genotype calls.

 verbose: Logical.

phenoData: 'phenoData' object or 'NULL'

 pkgname: alt. pdInfo package to be used

reference: logical, defaulting to TRUE ...

  tmpdir: Directory where temporary files are going to be stored at.

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

     'SnpCallSetPlus' object.

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

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

