qualityReport          package:tilingArray          R Documentation

_A_s_s_e_s_s _q_u_a_l_i_t_y _o_f _n_o_r_m_a_l_i_z_e_d _p_o_l_y-_A-_R_N_A _s_a_m_p_l_e_s

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

     Function to analyze quality of (normalized) tiling array data.
     Provides plots of intensities along the chromosome around
     specified genes, scatterplots comparing raw and normalized data,
     and a histogram of z-scores for intensities within annotated
     coding DNA regions.

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

     qualityReport(x, hybeType, normRef = NULL, compress = TRUE, selectGenes, 
       gff, probeAnno, output = "HTML", outputDir = ".", verbose = TRUE)

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

       x: tiling array data, either a character vector, naming the CEL
          files to analyze, OR an 'AffyBatch' containing the
          unnormalized data

hybeType: character string, naming the type of hybridized data, either
          'direct' for directly hybridized RNA (no normalization
          necessary) or 'reverse' for reverse-transcribed RNA

 normRef: samples used for normalization of the data, either a
          character vector naming the CEL-files to use for
          normalization of 'x' of an 'AffyBatch' containing the
          expression data of those samples. 'NULL' means 'no
          normalization'

compress: logical; if 'x' and 'normRef' were provided as character
          vectors, are the related CEL-files compressed?

selectGenes: character vector; for which genes are along-chromosome
          plots to be prepared

     gff: data frame with genome annotation from the GFF file.

probeAnno: environment with probe annotations

  output: character string, type of output to produce, currently only
          'HTML' is supported.

outputDir: path to storage directory of quality reports

 verbose: logical, do you want extended progess output to STDOUT?

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

     This function is called for producing quality reports in a
     specified format and does not return anything.

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

     Wolfgang Huber

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

