tilingArray-package       package:tilingArray       R Documentation

_t_i_l_i_n_g_A_r_r_a_y _p_a_c_k_a_g_e _o_v_e_r_v_i_e_w

_D_e_s_c_r_i_p_t_i_o_n:

     tilingArray package overview

_D_e_t_a_i_l_s:

     The package provides some functionalities that can be useful for
     the analysis of high-density tiling microarray data (such as
     Affymetrix genechips) for measuring transcript abundance and
     architecture. The main functionalities of the package are:

        *  The segmentation class for representing partitionings of a
           linear series of data (such as microarray intensity readings
           along a chromosome strand).

        *  The function 'segment' for fitting piecewise constant models
           using a dynamic programming algorithm that is both fast and
           exact, and 'confint' for calculating confidence intervals
           using the strucchange package. Please see the vignette
           _Segmentation demo_ in the file inst/doc/segmentation.pdf
           (source file inst/scripts/segmentation.Rnw).

        *  The function 'plotAlongChrom' for generating pretty plots of
           segmentations along with genomic features. Please also see
           the vignette _Segmentation demo_.

        *  The function 'normalizeByReference' for probe-sequence
           dependent response adjustment from  a (set of) reference
           hybridizations. Please see the vignette _Assessing
           signal/noise ratio before and after normalization_ in the
           file inst/doc/assessNorm.pdf (source file
           inst/scripts/assessNorm.Rnw).

_A_u_t_h_o_r(_s):

     W. Huber <huber@ebi.ac.uk>

