ExonArray-class         package:GenomeGraphs         R Documentation

_C_l_a_s_s "_E_x_o_n_A_r_r_a_y" _r_e_p_r_e_s_e_n_t_i_n_g _p_r_o_b_e _l_e_v_e_l _e_x_o_n _a_r_r_a_y _d_a_t_a _f_r_o_m _A_f_f_y_m_e_t_r_i_x

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

     Represents probe level exon array data from Affymetrix. Makes it
     possible to visualize alternative splicing as measured by the
     Affymetrix exon array platform and relate it to known transcript
     isoforms annotated by Ensembl

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("ExonArray",
     ...)'.

_S_l_o_t_s:


     '_i_n_t_e_n_s_i_t_y': Object of class '"matrix"', array data matrix
          containing probes  as the rows and samples as the columns

     '_p_r_o_b_e_S_t_a_r_t': Object of class '"numeric"' vector with the start
          positions of the probes

     '_p_r_o_b_e_E_n_d': Object of class '"numeric"' vector with the end
          positions of the probes

     '_p_r_o_b_e_I_d': Object of class '"character"' vector containing the
          probeset identifiers

     '_n_P_r_o_b_e_s': Object of class '"numeric"' vector defining how many
          probes there are for each exon/probeset

     '_s_i_z_e': Object of class '"numeric"' specifying the size of the
          ExonArray plot in the final plot

     '_d_i_s_p_l_a_y_P_r_o_b_e_s_e_t_s': Object of class '"logical"' used to indicate
          if probe set names should be plotted or not

     '_p_r_o_b_e_s_e_t_S_i_z_e': Object of class '"numeric"' font size of the
          probeset identifiers to be plotted 

     '_c_o_l_o_r': Object of class '"character"' vector of colors or one
          color that will be used to draw  the intensity values 

     '_m_a_p_C_o_l_o_r': Object of class '"character"' specifying the color of
          the lines that  map the probeset positions to the Ensembl
          gene annotation

     '_l_w_d': Object of class '"numeric"' vector of line widths to be
          used to plot the intensity data.

     '_l_t_y': Object of class '"character"' vector of line types to be
          used to plot the intensity data.

_E_x_t_e_n_d_s:

     Class '"gdObject"', directly.

_M_e_t_h_o_d_s:


     _s_h_o_w 'signature(object = "ExonArray")': ... 

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

     Steffen Durinck

_R_e_f_e_r_e_n_c_e_s:

     http://www.stat.berkeley.edu/~steffen/

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

     objects to See Also as 'gdPlot'

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

     if(interactive()){
     data("unrData", package="GenomeGraphs")
     library(biomaRt)
     mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

     title = new("Title", title ="ENSG00000009307", dp = DisplayPars(color = "darkslategray"))
     exmapcol = rep("khaki", length(unrNProbes))
     exmapcol[28]="darkred"
     probeSetCol = rep("grey", length(unrNProbes))
     probeSetCol[27:28]="darkslategray"
     probeSetLwd = rep(1, length(unrNProbes))
     probeSetLwd[27:28]=3

     exon = new("ExonArray", intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = exmapcol, probeSetColor = probeSetCol, probeSetLwd = probeSetLwd), displayProbesets=FALSE)
     exon2 = new("ExonArray", intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = exmapcol, probeSetColor = probeSetCol, probeSetLwd = probeSetLwd, plotMap=FALSE), displayProbesets=TRUE)

     affyModel = new("GeneModel", exonStart = unrPositions[,3], exonEnd =  unrPositions[,4])
     gene = new("Gene", id = "ENSG00000009307", biomart = mart)
     transcript = new("Transcript", id ="ENSG00000009307" , biomart = mart)
     legend = new("Legend", legend = c("affyModel","gene"), dp = DisplayPars(color= c("darkgreen","orange")))

     gdPlot(list(title,exonarray1 = exon2,exonarray2= exon, AffymetrixModel= affyModel, gene, transcript, legend), minBase = min(exon@probeStart), maxBase=max(exon@probeEnd))
     }

