bgcorrect                package:xps                R Documentation

_B_a_c_k_g_r_o_u_n_d _C_o_r_r_e_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Background corrects probe intensities in an object of class
     'DataTreeSet'.

_U_s_a_g_e:

     bgcorrect(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(0), option = character(0), exonlevel = "", params = list(), verbose = TRUE)

     bgcorrect.gc(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", select = "antigenomic", verbose = TRUE)

     bgcorrect.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", verbose = TRUE)

     bgcorrect.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", verbose = TRUE)

     bgcorrect.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", verbose = TRUE)

     xpsBgCorrect(object, ...)

_A_r_g_u_m_e_n_t_s:

xps.data: object of class 'DataTreeSet'.

filename: file name of ROOT data file.

 filedir: system directory where ROOT data file should be stored.

  tmpdir: optional temporary directory where temporary ROOT files
          should be stored.

  update: logical. If 'TRUE' the existing ROOT data file 'filename'
          will be updated.

  select: type of probes to select for background correction.

  method: background method to use.

  option: type of background correction to use.

exonlevel: exon annotation level determining which probes should be
          used for summarization; exon/genome arrays only.

  params: vector of parameters for background method.

 verbose: logical, if 'TRUE' print status information.

  object: object of class 'DataSet'.

     ...: the arguments described above.

_D_e_t_a_i_l_s:

     Background corrects probe intensities in an object of class
     'DataTreeSet'.

     'xpsBgCorrect' is the 'DataSet' method called by function
     'bgcorrect', containing the same parameters.

_V_a_l_u_e:

     An 'DataTreeSet'

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'express'

_E_x_a_m_p_l_e_s:

     ## first, load ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     ## MAS4 sector background
     data.bg.mas4 <- bgcorrect.mas4(data.test3,"tmp_Test3MAS4Bgrd",filedir=getwd(),tmpdir="",verbose=FALSE)

     ## need to attach background intensities
     data.bg.mas4 <- attachBgrd(data.bg.mas4)

     ## get data.frame
     bg.mas4 <- validBgrd(data.bg.mas4)
     head(bg.mas4)

     ## plot images
     if (interactive()) {
     image.dev(data.bg.mas4,bg=TRUE,col=rainbow(32))
     image(matrix(bg.mas4[,1], ncol=ncols(schemeSet(data.bg.mas4)), nrow=nrows(schemeSet(data.bg.mas4))))
     }

