matchAffyProbes          package:altcdfenvs          R Documentation

_M_a_t_c_h _t_h_e _p_r_o_b_e_s _o_n _a_n _A_f_f_y_m_e_t_r_i_x _a_r_r_a_y

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

     Match the individual probes on an Affymetrix array to arbitrary
     targets.

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

     mmProbes(probes)

     matchAffyProbes(probes, targets, chip_type,
                     matchmm = TRUE,
                     selectMatches = function(x) which(countIndex(x) > 0),
                     ...)

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

  probes: a 'probetable' object 

 targets: a vector of references 

chip_type: a name for the chip type.

 matchmm: whether to match MM probes or not

selectMatches: a function to select matches (see Details).

     ...: further arguments to be passed to 'matchPDict'.

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

     The matching is performed by the function 'matchPDict'. The man
     page for that function will indicate what are the options it
     accepts.

     In the case where a large number targets are given, like when each
     target represents a possible mRNA, is it expected to have a
     largely sparce incidence matrix, that is a low number of probes
     matching every target. For that reason, only the index of matching
     probes are associated with each given target, with the function
     'selectMatches' giving the definition of what are matching probes.
     The default function just count anything matching, but the user
     can specify a more stringent definition if wanted.

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

     'mmProbes' returns a vector of MM probe sequences.

     'matchAffyProbes' returns an instance of 'AffyProbesMatch-class'.

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

     Laurent Gautier

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

     'matchPDict' for details on how the matching is performed,
     'AffyProbesMatch-class' and 'buildCdfEnv.biostrings'

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

     library(hgu133aprobe)

     filename <- system.file("exampleData", "sample.fasta",
                             package="altcdfenvs")

     fasta.seq <- readFASTA(filename)

     targets <- unlist(lapply(fasta.seq, "[[", "seq"))
     names(targets) <- lapply(fasta.seq, "[[", "desc")
     names(targets) <- sub("^>.+\\|(NM[^ \\|]+|Hs[^ \\|]+)\\|? .+$", "\\1",
                           names(targets))

     m <- matchAffyProbes(hgu133aprobe,
                          targets,
                          "HG-U133A")

