SeqFastaAA              package:seqinr              R Documentation

_A_A _s_e_q_u_e_n_c_e _i_n _F_a_s_t_a _F_o_r_m_a_t

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

     'as.SeqFastaAA' is called by the function as 'read.fasta'. It
     creates an object of class 'SeqFastaAA'.  'is.SeqFastaAA' returns
     TRUE if the object is of class 'SeqFastaAA'.  'summary.SeqFastaAA'
     gives the AA composition of an object of class 'SeqFastaAA'.

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

     as.SeqFastaAA(object, name = NULL, Annot = NULL)
     is.SeqFastaAA(object)
     summary.SeqFastaAA(object,...)

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

  object: a vector of chars representing a biological sequence 

    name: 'NULL' a character string specifying a name for the sequence 

   Annot: 'NULL' a character string specifying some annotations for the
          sequence 

     ...: additional arguments affecting the summary produced 

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

     'as.SeqFastaAA' returns an object sequence of class 'SeqFastaAA'.
     'summary.SeqFastaAA' returns a list which the following
     components: 

composition: the AA counting of the sequence

AA.Property: the percentage of each group of amino acid in the
          sequence. By example, the groups are small, tiny, aliphatic,
          aromatic ... 

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

     D. Charif

_R_e_f_e_r_e_n_c_e_s:

     'citation("seqinr")'

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

       s <- read.fasta(File = system.file("sequences/seqAA.fasta", package = "seqinr"), seqtype="AA")
       is.SeqFastaAA(s[[1]])
       summary(s[[1]])
       myseq <- s2c("MSPTAYRRGSPAFLV*")
       as.SeqFastaAA(myseq, name = "myseq", Annot = "blablabla")
       myseq

