Ttest                package:RNAither                R Documentation

_P_e_r_f_o_r_m _a _S_t_u_d_e_n_t'_s _t-_t_e_s_t

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

     Performs a Student's t-test on the intensity data.

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

     Ttest(dataset, listofargs)

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

 dataset: an R data frame generated with 'generateDatasetFile' 

listofargs: a list containing: 

          - ' "g"' (greater) for significant increase, ' "l"' (lower)
          for significant decrease, or ' "two.sided"' for both 

          - either a number indicating the true value of the mean, or a
          character string indicating the name of the gene to compare
          with 

          - a character string specifying the column whose values will
          be used for the test

          - a character string specifying the name of the dataset
          column to be used to define the replicate, e.g. ' "GeneName"'
          or ' "Internal_GeneID"' 

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

     Returns a list containing:

pValVec : a named vector of p-values

dataset : the dataset with an added column ' "p.value.mannwhitney"'

paste("pValue.ttest", testType, sep="_") : the character string
          '"pValue.ttest"' concatenated with the 'testType' (first
          element of 'listofargs')

"t test" : the character string '"t test"'

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

     'MannWhitney', 'RankProduct'

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")

     pvals1 <- Ttest(dataset, list("l", median(dataset$SigIntensity, na.rm=TRUE), "SigIntensity", "GeneName"))
     pValVec1 <- pvals1[[1]]
     scoredDataset1 <- pvals1[[2]]

