calcInOutDegStats          package:ppiStats          R Documentation

_T_h_i_s _f_u_n_c_t_i_o_n _c_a_l_c_u_l_a_t_e_s _t_h_e _v_a_r_i_o_u_s _d_e_g_r_e_e _s_t_a_t_i_s_t_i_c _f_o_r _a
_P_r_o_t_e_i_n-_P_r_o_t_e_i_n _I_n_t_e_r_a_c_t_i_o_n (_P_P_I) _G_r_a_p_h

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes a graphNEL argument and calculates several
     degree statistics for which further analysis can be made.

_U_s_a_g_e:

     calcInOutDegStats(graphObj, homodimer=FALSE)

_A_r_g_u_m_e_n_t_s:

graphObj: The argument 'graphObj' is an instance of the  class
          graphNEL.

homodimer: A logical. If FALSE, the function removes all homodimer
          relationships. It retains them otherwise.

_V_a_l_u_e:

     The return value is a list of various degree statistics of the PPI
     directed graph: 

inDegree: A named numeric vector. The names corresponds to the
          particular yeast Open Reading Frame (ORF), and each entry
          details how many edges flow towards that node, i.e. how many
          times each node was detected as a prey.

outDegree: A named numeric vector. The names corresponds to the
          particular yeast Open Reading Frame (ORF), and each entry
          details how many edges flow out from that node, i.e. how many
          prey was detected by each node as a bait.

inDegreeMinusOutDegree: A named numeric vector. This entry is the
          inDegree minus the outDegree entries, or the signed
          difference for each node as a prey to  each node as a bait.

outDegreeMinusInDegree: A named numeric vector. This entry is the
          outDegree minus the inDegree entries, or the signed
          difference for each node as a bait to  each node as a prey.

recipInDegree: A named numeric vector. Again the names represents the
          ORFs, while each entry corresponds to how many times each
          node was found as a prey in a  reciprocated interaction.

recipOutDegree: A named numeric vector. Again the names represents the
          ORFs, while each entry corresponds to how many times each
          node was found as a bait in a  reciprocated interaction.

totalRecipDegree: A numeric. For the PPI graph given, this argument
          gives the total number of reciprocated interactions found.

unrecipInDegree: A named numeric vector. The names corresponds ORF and 
          each entry details how many edges flow towards each node
          modulo the reciprocated  interactions, i.e. for each node
          $p$, how many baits $b$ detected $p$ as a prey with  the
          condition that $p$ never detects $b$ as a prey.

unrecipOutDegree: A named numeric vector. The names corresponds ORF and
           each entry details how many edges flow out from each node
          modulo the reciprocated  interactions, i.e. for each node
          $b$, how many prey $p$ does $b$ detect with the  condition
          that $b$ is never detected by $p$.

totalUnrecipDegree: A numeric. The total number of unreciprocated
          interactions for the PPI graph given.

     ...

_A_u_t_h_o_r(_s):

     T Chiang

_E_x_a_m_p_l_e_s:

             library(ppiData)
             degStat <- calcInOutDegStats(Cagney2001BPGraph)
             degStat$recipOutDeg

