screenMatch             package:cellHTS             R Documentation

_M_a_t_c_h_i_n_g _t_h_e _g_e_n_e _a_n_n_o_t_a_t_i_o_n _o_f _t_w_o _s_c_r_e_e_n_s

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

     Match the annotation of two 'cellHTS' objects in order to find the
     common  gene-perturbing reagents

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

     screenMatch(screens, ids)

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

 screens: a list of annotated cellHTS objects.

     ids: a character vector of length two giving, for each cellHTS
          object, the name of the column of slot 'geneAnno' that should
          be used for the annotation IDs. See details.

_D_e_t_a_i_l_s:

     By default, if 'ids' is missing, the column 'GeneID' of the slot
     'geneAnno' of each of the 'cellHTS' objects in 'screens' is taken
     for the annotation IDs when comparing the two data sets.

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

     A list with two components: 

p.overlap: a vector giving the proportion of overlap in the screens'
          annotation.

isInBoth: a list of logical vectors, each of which with length equal to
          the product between 'nr. Well' and 'nr. Plates' in each
          screen, indicating whether the respective gene-perturbing
          reagent of that screen is also present in the other.

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

     Ligia Braz ligia@ebi.ac.uk

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

         ## Just for exemplification purposes, we consider the complete genome-wide screen "KcViab" 
         ## and its first 3 plates ("KcViabSmall"): 
         data(KcViab)
         data(KcViabSmall)
         screens <- list(KcViab, KcViabSmall)
         out <- screenMatch(screens)
         out$p.overlap
         sapply(out$isInBoth, sum)
         sapply(1:2, function(z) table(screens[[z]]$geneAnno$Plate[out$isInBoth[[z]]]))

