seqSkew                package:GeneR                R Documentation

_c_o_m_p_u_t_e _t_h_e _s_t_r_a_n_d _a_s_s_y_m_e_t_r_i_e_s _f_r_o_m _o_n_e _s_e_q_u_e_n_c_e _f_r_a_g_m_e_n_t

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

     compute the strand assymetries from one sequence fragment

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

     seqSkew(seqno = 0, from=1,to=0,strand=getStrand(),case = "all")
     GCcontent(seqno = 0, from=1,to=0,case = "all",...)

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

   seqno: Input sequence number. (bufseq)

 from,to: Begining and ending of sequence, can be vectors. 0 represent
          the last nucleotide and 1 the first one.

    case: "all"

  strand: strand

     ...: other parameters

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

     a data frame with 4 columns as follow 

TA skew or TA pourcent: (T-A)/(T+A) or count(TA) / count(TAGCN)

GC skew or GC pourcent: (G-C)/(G+C) or count(GC) / count(TAGCN)

total skew or C pourcent: TA+GC skews or count(C) / count(TAGCN)

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

     Yves d'Aubenton and Emna

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

     'densityProfile','bankDensityProfile','compoSeq'

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

          s<-"CGTACGTAGTAGCTAGCTAGCTAGCTAGCTGATCGATGCTAGCTGATCGATGCT"
          placeString(s,seqno=0)
          x<-c(1,8,15,50)
          y<-c(5,12,19,54)
          seqSkew(seqno=0,from=x,to=y,strand=0)

          seqSkew(seqno=0,from=x,to=y,strand=1)

          GCcontent(seqno=0,from=x,to=y)

