computeSlidingT            package:Ringo            R Documentation

_F_u_n_c_t_i_o_n _t_o _c_o_m_p_u_t_e _s_l_i_d_i_n_g _T _s_t_a_t_i_s_t_i_c_s _o_n _a _t_i_l_i_n_g _e_x_p_r_e_s_s_i_o_n _s_e_t

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

     Function to compute sliding (regularized) one- or two-sample T
     statistics on a tiling expression set.

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

     computeSlidingT(xSet, probeAnno, allChr = c(1:19, "X", "Y"), test = "one.sample", grouping = NULL, winHalfSize = 400, min.probes = 5, checkUnique = TRUE, uniqueCodes = c(0), verbose = TRUE)

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

    xSet: Object of class 'ExpressionSet' holding the normalized probe
          intensity data

probeAnno: Environment holding the genomic positions of probes in the
          ExpressionSet

  allChr: Character vector of all chromosomes in genome

    test: character; one of 'one.sample' or 'two.sample'

grouping: factor vector of length equal to number of samples, currently
          not required

winHalfSize: Half the size of the window centered at a probe position,
          in which all other probes contribute to the calculation of
          the mean and standard deviation.

min.probes: integer; if less probes are in the sliding window, NA
          instead of the mean and sd is returned. This is meant to
          avoid to  computing non-meaningful means and standard
          deviations. If unwanted, set this to 1 or less

checkUnique: logical; indicates whether the uniqueness indicator of
          probe matches from the probeAnno environment should be used.

uniqueCodes: numeric; which numeric codes in the chromosome-wise
          match-uniqueness elements of the probeAnno environment
          indicate uniqueness?

 verbose: logical; detailed progress output to STDOUT?

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

     An object of class 'ExpressionSet', holding the T statistics
     values for the probes of the supplied ExpressionSet. The number of
     results samples is the number of levels in the supplied factor
     'grouping'.

_N_o_t_e:

     the option 'two.sample' is not implemented yet

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

     Joern Toedling toedling@ebi.ac.uk

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

     'sliding.meansd'

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

      exDir <- system.file("exData",package="Ringo")
       load(file.path(exDir,"exampleProbeAnno.rda"))
       load(file.path(exDir,"exampleX.rda"))
       tX <- computeSlidingT(exampleX, probeAnno=exProbeAnno,
                  allChr=c("9"), winHalfSize=400)
       sampleNames(tX) <- "t-Stat_Suz12vsTotal"
       if (interactive()){
         par(mfrow=c(1,1))
         chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000), ylim=c(-2,8.5), probeAnno=exProbeAnno, gff=exGFF)
         chipAlongChrom(tX, chrom="9", xlim=c(34318000,34321000),
     probeAnno=exProbeAnno, itype="l", ilwd=4, paletteName="Spectral",
     add=TRUE)
       }

