compareHits             package:RNAither             R Documentation

_S_e_a_r_c_h_i_n_g _f_o_r _c_o_m_m_o_n _h_i_t_s _b_e_t_w_e_e_n _d_i_f_f_e_r_e_n_t _s_c_o_r_i_n_g _m_e_t_h_o_d_s

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

     Searches for common hits between different scoring methods.

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

     compareHits(hitVec1, hitVec2, namesHitVec1, namesHitVec2)

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

hitVec1, hitVec2: the two binary hit vectors to be compared 

namesHitVec1, namesHitVec2: the names of the siRNAs corresponding to
          the hit vectors 

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

     Returns a character vector indicating which siRNAs are identified
     as hits in two different hit scoring schemes.

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

     'vennDiag' , 'Ttest', 'MannWhitney'

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

     data(scoredDataset1, package="RNAither")
     data(pValVec1, package="RNAither")

     data(scoredDataset2, package="RNAither")
     data(pValVec2, package="RNAither")

     ##for details on the generation of pValVec and scoredDataset,
     ##see the examples of the functions Ttest and MannWhitney linked above.

     scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Hits1", 0.05, 
     "GeneName", "pvalue_testfile1.txt")
     scoredHits2 <- hitselectionPval(scoredDataset2, pValVec2, "SigIntensity", "Hits2", 0.05, 
     "GeneName", "pvalue_testfile2.txt")

     hitVector1 <- scoredHits1[[2]]
     hitVector2 <- scoredHits2[[2]]

     common_hits <- compareHits(hitVector1, hitVector2, names(hitVector1), names(hitVector2))

