backgroundEstimate       package:beadarraySNP       R Documentation

_E_s_t_i_m_a_t_e _b_a_c_k_g_r_o_u_n_d _i_n_t_e_n_s_i_t_i_e_s _f_r_o_m _f_o_r_e_g_r_o_u_n_d _i_n_t_e_n_s_i_t_y

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

     Background intensity from Illumina Golden Gate bead arrays are
     estimated based on several data models

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

       backgroundEstimate(object,method=c("minimum","mode","intmin","anglemode"),
       maxmode=3000,bincount=40,maxangle=0.3,subsample="OPA")

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

  object: SnpSetIllumina object

  method: chracter, data model to use

 maxmode: numeric, maximum intensity for mode for 'method="mode"'

bincount: numeric, for 'method="intmin"' , see details

maxangle: numeric in radians, maximum theta for mode for
          'method="anglemode"' 

subsample: factor or column name in 'featureData' slot

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

     The Illumina software does not provide background values in the
     output.  Some models can be used to estimate background from the
     raw data intensities.
      'minimum': The allele specific minimum intensity is used.
      'mode': This model assumes that the first mode of the density of
     the  intensities is determined by the zero-allele in the data, see
     ref. The  signal intensity of the zero-allele should be zero,
     therefore this is  considered the background value.
      'intmin': This model assumes there is crosstalk between the
     alleles, and  background increases with the intensity of the other
     allele. The range  between 0 and the maximum of the other allele
     is divided in 'bincount' bins, and the minimum for this allele is
     determined for probes where the  other allele falls in a bin. A
     linear fit is determined though the minimum values to obtain a
     gradually increasing value.
      'anglemode': This model finds the density modes closest to 0 and
     $\frac{pi}{2}$   for polar transformed intensities, and uses this
     to determine background.

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

     This function returns an 'SnpSetIllumina' object. The 'Rb' and
     'Gb'  matrices in the 'assayData' slot contain estimated
     background values.

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

     Jan Oosting

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

     'SnpSetIllumina-class', 'backgroundCorrect.SNP'

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

