AnalyzeTilingCelFiles       package:AffyTiling       R Documentation

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

     AnalyzeTilingCelFiles extracts intensity data from a group of CEL
     files and returns annotated intensities using information from a
     BPMAP file. Options can be set to limit the analysis to certain
     genomic features or regions of interest,thus requiring less memory
     and computing time.

     By default, preforms background correction, quantile
     normalization, and log2 transform.  This can be disabled by
     setting ReturnRawIntensities to TRUE, if raw intensity values are
     desired.

     This function returns a matrix, where rows represent probes and
     columns represent the following values: -Unique probe ID -Probe
     start position (in genomic coordinates) -Chromosome -Sequence
     -Intensity for sample 1 -Intensity for sample 2 ... -Intensity for
     sample N

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

     AnalyzeTilingCelFiles(CEL_filenames, BPMAP_filename, outfilename=NULL, iID=NULL, iCHR=NULL, iSTART=NULL, iEND=NULL, makeUniqueID=TRUE, readOnlyNCBI=TRUE, readProbeSeq=FALSE, IgnoreBpmapCelPlatformMismatch=FALSE, ReturnRawIntensities=FALSE)

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

CEL_filenames: A character vector of the path to all CEL file(s) in the
          analysis. 

BPMAP_filename: The path to the BPMAP file which describes the arrays
          specified in the cel files. 

outfilename: If specified, the function writes a tab-separated table of
          normalized intensities. 

     iID: Vector of IDs for each interval specified. 

    iCHR: Vector of chromosomes for each interval. 

  iSTART: Integer vector of the interval start. 

    iEND: Integer vector of the interval end. 

makeUniqueID: If TRUE (default), returns a column of unique identifiers
          for each probe, of the form: chr-start. 

readOnlyNCBI: If TRUE (default), returns ONLY probes that target NCBI
          sequences, TIGR and Affymetrix controls are ignored. 

readProbeSeq: If TRUE, returns the first 25 bp of the probe sequence. 

IgnoreBpmapCelPlatformMismatch: If TRUE, ignores a mismatch between
          BPMAP and CEL platforms. (EXPERT ONLY!) 

ReturnRawIntensities: If TRUE, returns raw intensity values associated
          with the specified regions.  Otherwise (default) preforms
          RMA-like processing of data using the affy package. 
          Processing includes background correction, quantile
          normalization, and a log-2 transform. 

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

     Charles Danko

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

     ## Note that executing the following example requires .bpmap and .cel files in the working directory.
     ## If these files do not, the program will not execute.

     ## Get the file names in the current working directory.
     CEL_NAMES <- dir(pattern=".CEL|.cel");
     BPMAP     <- dir(pattern=".bpmap");

     ## If files are found in the current working directory ... start the analysis!!
     if( (NROW(CEL_NAMES) > 0) & (NROW(BPMAP) > 0) ) {
       AnalyzeTilingCelFiles(CEL_NAMES, BPMAP, outfilename="NormalizedData.tsv");
     }

