aCGH.read.Sprocs            package:aCGH            R Documentation

_C_r_e_a_t_e _o_b_j_e_c_t _o_f _c_l_a_s_s "_a_C_G_H" _f_r_o_m _S_p_r_o_c _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function reads in two-channel Array Comparative Genomic
     Hybridization Sproc files, flags them for bad quality and missing
     data, and creates object of class 'aCGH'.

_U_s_a_g_e:

     aCGH.read.Sprocs(fnames, latest.mapping.file = NULL, maxsd = 0.2,
                      minreplic = 2, chrom.remove.threshold = 24,
                      prop.missing = 0.25, sample.names = fnames,
                      sample.quality.threshold = 0.4,
                      cols = c("Log2Rat", "Log2StdDev", "NReplic", "Bad.P"),
                      unmapScreen=TRUE, dupRemove = TRUE)

_A_r_g_u_m_e_n_t_s:

  fnames: a vector of character strings containing the file names of
          each Sproc data file.

latest.mapping.file: The name of an optional file that contains newer
          clone mapping different from the clone mapping used at the
          time when the arrays were created.

   maxsd: maximum of standard deviation of log2 ratios used in
          pre-filtering.

minreplic: minimum number of replicates per clone for a single chip
          used to calculate the log2 ratios.

chrom.remove.threshold: Chromosomes are ordered and numbered as usual,
          except for X and Y chromosome, which in for Homo sapiens
          genome have numbers 23 and 24 repsectivelly, in for Mus
          musculus 20 and 21, etc.

prop.missing: Clones are screened out and if the proportion missing in
          the samples is 'prop.missing' they are removed.

sample.names: Sample names. If they are missing, the file names are
          used after stripping the characters after the last dot in the
          filename if one exists; for example 'myfile.txt' becomes
          myfile.

sample.quality.threshold: Mark those samples that have their proportion
          of missing values 'sample.quality.threshold'.

    cols: character vector of length 4 containing the following Sproc
          file column names: log2 ratios, std. deviations of the log2
          ratios, number of replicates for each clone and flags for bad
          clones. Defaults to c("Log2Rat", "Log2StdDev", "NReplic",
          "Bad.P"). Note that all the whitespace characters in the
          column names will be replaced with dots.

unmapScreen: Indicator for whether clones with incomplete mapping
          information should be removed from the dataset. Note that
          leaving them in may cause plotting routines fail. Defaults to
          TRUE

dupRemove: Indicator for whether clones with duplicate names should be
          averaged and removed from the dataset leaving only one
          occurence of each duplicated set.Defaults to TRUE

_V_a_l_u_e:

     Object of class 'aCGH'.

_A_u_t_h_o_r(_s):

     Jane Fridlyand, Peter Dimitrov

_S_e_e _A_l_s_o:

     'aCGH'

_E_x_a_m_p_l_e_s:

     datadir <- system.file("examples", package = "aCGH")
     latest.mapping.file <-
           file.path(datadir, "human.clones.info.Jul03.txt")
     ex.acgh <-
             aCGH.read.Sprocs(dir(path = datadir,pattern = "sproc",
                             full.names = TRUE), latest.mapping.file,
                             chrom.remove.threshold = 23)
     ex.acgh

     ## Testing if creating the object went right. Should all be true.

     all(log2.ratios(ex.acgh)[ 1, ] == c(-0.077698 , 0.007389))
     clone.name <- "HumArray2H10_T30"
     all(log2.ratios(ex.acgh)[ clone.name, ] == c(0.025567 , -0.036908))

