TilingCelFiles2Probesets     package:AffyTiling     R Documentation

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

     TilingCelFiles2Probesets 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.

     Returns a matrix, where rows represent probe sets and columns
     represent the following:   -Unique probeset ID ("chromosome-first
     probe START position-last probe END position") -Probe start
     position (in genomic coordinates) -Chromosome -Average normalized
     intensity for sample 1 -Average normalized intensity for sample 2
     ... -Average normalized intensity for sample N

     Note that unlike AnalyzeTilingCelFiles, this function reports only
     1 average value for all probes in each interval.

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

     TilingCelFiles2Probesets(CEL_filenames, BPMAP_filename, outfilename=NULL, iID=NULL, iCHR, iSTART, iEND, IgnoreBpmapCelPlatformMismatch=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.  If NULL (default)
          creates a unique ID for each interval of the form:
          "CHR-START-END". 

    iCHR: Vector of chromosomes for each interval. 

  iSTART: Integer vector of the interval start. 

    iEND: Integer vector of the interval end. 

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

_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.

     ## Creates a sample interval of the first 1MB of chromosome 1-3.
     ## This function will return a single value for each interval.
     iCHR <- c("chr1", "chr2", "chr3")
     iSTART <- rep(1, 3)
     iEND <- iSTART + 1e+06

     ## 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) ) {
       TilingCelFiles2Probesets(CEL_NAMES, BPMAP, outfilename="NormalizedData.tsv", iID=NULL, iCHR=iCHR, iSTART=iSTART, iEND=iEND);
     }

