MATScore                package:rMAT                R Documentation

_D_e_t_e_c_t_i_o_n _o_f _e_n_r_i_c_h_e_d _r_e_g_i_o_n_s

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

     This function is used to compute the rMAT scores following
     normalization of expression values in order to locate putative
     enriched regions.

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

     MATScore(tilingSet, cName="NULL", dMax=600,nProbesMin=8, dMerge=300,method="score",threshold=5,verbose=FALSE,bedName="NULL")
           

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

tilingSet: This object contains an ExpressionSet

   cName: Unique identifier of control name

    dMax: An integer value. The sliding window side of which the
          adjacent probes are to average upon in order to compute the
          rMAT score.

nProbesMin: An integer value. The minimum number of probes to average
          upon. If the number of probes within the interval is less
          than nProbesMin, the rMAT score of the region will not be
          computed.

  dMerge: An integer value. The maximum size to merge adjacent probes
          and categorize them as one region for scores of  adjacent
          probes uniformly above the input threshold.

  method: A character string value equal to "score", "pValue" or "FDR".
          "score" denotes the method of calling enriched regions based
          sliding widow scores. "pValue" denotes the method of calling
          enriched regions based on p-values. Method "FDR" uses an FDR
          procedure to call regions. See Details below.

threshold: An integer value. The threshold of rMAT Score to be labeled
          as an enriched region. For method=1 or 3, the higher the
          score, the more confident we are about enriched regions. For
          method=2, the lower the score, the more confident we are
          about enriched regions.

 verbose: A logical value. If verbose is TRUE, progress information
          would be displayed.

 bedName: This file file includes columns "chromosome rMATScore region
          pValue" for each probe.

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

     For more details on the calculation of the rMAT score, pvalues,
     etc, please refer to the following paper: Johnson et al.
     Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl
     Acad Sci USA (2006) vol. 103 (33) pp. 12457-62

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

     The rMAT Score, pValues, and regions. For the regions vector, let
     0 denotes the unenriched region. If an enriched region is found,
     the interval of the region is labeled by a none 0 value. The first
     region detected is labeled 1 and the next regions are subsequently
     incremented.

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

     Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo,
     raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca

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

     'NormalizeProbes()' for normalizing expression values before
     computing the rMAT enriched regions.

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

     ####################################################
     #The data are in inst/doc folder in rMAT package.
     ####################################################

     pwd<-"" #INPUT FILES- BPMAP, ARRAYS, etc.
     path<- system.file("doc/Sc03b_MR_v04_10000.bpmap",package="rMAT")

     bpmapFile<-paste(pwd,path,sep="")

     pathCEL<- system.file("doc/Swr1WTIP_Short.CEL",package="rMAT")
     arrayFile<-paste(pwd,c(pathCEL),sep="")

     # Show the all the different sequences
     ReadBPMAPAllSeqHeader(bpmapFile)

     # create a tiling Set from the corresponding data
     # This will only grep the sequences with Sc
     ScSet<-BPMAPCelParser(bpmapFile, arrayFile, verbose=FALSE,groupName="Sc")     

     # show the object
     show(ScSet)

     # summarize its content
     summary(ScSet)

     ScSetNorm<-NormalizeProbes(ScSet, method="MAT",robust=FALSE, all=FALSE, standard=TRUE, verbose=FALSE)
             
     ScScore<- MATScore(ScSetNorm, cName=NULL, dMax=600,nProbesMin=8, dMerge=300,method="score",threshold=5,verbos=TRUE,bedName="MyBedFile") 
             

