write.table             package:KCsmart             R Documentation

_W_r_i_t_e _s_u_m_m_a_r_y _o_f _t_h_e _s_i_g_n_i_f_i_c_a_n_t _r_e_g_i_o_n_s _t_o _a _t_a_b_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Write summary of the significant regions to a table

_U_s_a_g_e:

     write.table(x, file, append, quote, sep, eol, na, dec, row.names, col.names, qmethod)
     ## S4 method for signature 'sigSegments':
     write.table(x, file="", append = FALSE, quote = 7, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = TRUE, col.names=c("Status", "Chromosome", "Start", "End", "Average KC score", "Mode KC score", "Probes"), qmethod = c("escape", "double"))

_A_r_g_u_m_e_n_t_s:

       x: The sigSegments object to be summarized

    file: either a character string naming a file or a connection open
          for writing.  '""' indicates output to the console.

  append: logical. Only relevant if 'file' is a character string.  If
          'TRUE', the output is appended to the file.  If 'FALSE', any
          existing file of the name is destroyed.

   quote: a logical value ('TRUE' or 'FALSE') or a numeric vector.  If
          'TRUE', any character or factor columns will be surrounded by
          double quotes.  If a numeric vector, its elements are taken
          as the indices of columns to quote.  In both cases, row and
          column names are quoted if they are written.  If 'FALSE',
          nothing is quoted.

     sep: the field separator string.  Values within each row of 'x'
          are separated by this string.

     eol: the character(s) to print at the end of each line (row).

      na: the string to use for missing values in the data.

     dec: the string to use for decimal points in numeric or complex
          columns: must be a single character.

row.names: either a logical value indicating whether the row names of
          'x' are to be written along with 'x', or a character vector
          of row names to be written.

col.names: either a logical value indicating whether the column names
          of 'x' are to be written along with 'x', or a character
          vector of column names to be written.  See the section on
          'CSV files' for the meaning of 'col.names = NA'.

 qmethod: a character string specifying how to deal with embedded
          double quote characters when quoting strings.  Must be one of
          '"escape"' (default), in which case the quote character is
          escaped in C style by a backslash, or '"double"', in which
          case it is doubled.  You can specify just the initial letter.

_D_e_t_a_i_l_s:

     Writes a summary of the sigSegments object to file. The resulting
     table contains 7 columns. The interpretation of the columns is as
     follows:

_S_t_a_t_u_s Either 'L' for loss or 'G' for gain

_C_h_r_o_m_o_s_o_m_e The chromosome on which this segment is located

_S_t_a_r_t The start position (in base pairs) of the segment on the
     chromosome

_E_n_d The end position of the segment on the chromosome

_A_v_e_r_a_g_e _K_C _s_c_o_r_e The average KCsmart score over all base pairs in this
     segment

_M_o_d_e _K_C _s_c_o_r_e The highest (for gains) or lowest (for losses) KCsmart
     score over all base pairs in this segment

_P_r_o_b_e_s All probes from the original data that fall into this segment

_A_u_t_h_o_r(_s):

     Jorma de Ronde

_S_e_e _A_l_s_o:

     'calcSpm', 'getSigSegments'

_E_x_a_m_p_l_e_s:

     data(hsSampleData)
     data(hsMirrorLocs)

     spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

     siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)

     sigSegments1mb <- getSigSegments(spm1mb, siglevel1mb)
     write.table(sigSegments1mb, file=file.path(tempdir(),'sigSegments1mb.txt'))

