createIndex            package:ArrayTools            R Documentation

_C_r_e_a_t_i_n_g _a_n _H_T_M_L _i_n_d_e_x _f_i_l_e

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

     This HTML index file will link all the ouputted result, including
     Quality Assessment Report, differentially expressed genes, etc...

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

     createIndex(..., mydir = getwd(), index.file = "index.html", createHeader = NULL)

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

     ...: regressionResults or interactionResult

   mydir: the directory to contain the index file 

index.file: name of the index file 

createHeader: If want to want to create an Header, such as your name,
          company names, etc...

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

     creating an HTML index-file in your directory

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

     Xiwei Wu, Arthur Li

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

     data(eSetExample)
     design<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment")
     contrast<- new("contrastMatrix", design.matrix = design, 
         compare1 = "Treated", compare2 = "Control")
     result<- regress(eSetExample, contrast)
     sigResult<- selectSigGene(result, fc.value=log2(2)) 
     ## Not run: Output2HTML(sigResult)

     design.int<- new("designMatrix", target=pData(eSetExample), covariates = c("Treatment", "Group"),
         intIndex = c(1, 2))
     contrast.int<- new("contrastMatrix", design.matrix = design.int, interaction=TRUE)
     result.int<- regress(eSetExample, contrast.int)
     sigResult.int <- selectSigGene(result.int)
     intResult <- postInteraction(eSetExample, sigResult.int, mainVar ="Treatment",
        compare1 = "Treated", compare2 = "Control")
     sigResultInt <- selectSigGeneInt(intResult)
     ## Not run: Output2HTML(sigResultInt)

     ## Not run: createIndex(sigResult, sigResultInt, createHeader = c("Arthur Li", "COH"))

