BGAfun                package:bgafun                R Documentation

_B_G_A_f_u_n _A _m_e_t_h_o_d _t_o _i_d_e_n_t_i_f_y _s_p_e_c_i_f_i_t_y _d_e_t_e_r_m_i_n_i_n_g _r_e_s_i_d_u_e_s _i_n _p_r_o_t_e_i_n _f_a_m_i_l_i_e_s

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

     This Package combines between group analysis with sequence
     alignments to identify specifity determining residues in protein
     families

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

     Iain Wallace <iain.wallace@ucd.ie>

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

     Wallace, I.M. and Higgins, D.G. (2007) Supervised multivariate
     analysis of sequence groups to identify specificity determining
     residues, BMC Bioinformatics, 8, 135.

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

     library(bgafun)
     #read in alignment
     LDH <- read.alignment(file = system.file("sequences/LDH-MDH-PF00056.fasta", package = "bgafun"), format = "fasta")

     #Assign into groups
     LDH.amino=convert_aln_amino(LDH)
     LDH.groups=rownames(LDH.amino)
     LDH.groups[grep("LDH",LDH.groups)]="LDH"
     LDH.groups[grep("MDH",LDH.groups)]="MDH"
     LDH.groups=as.factor(LDH.groups)

     #Convert to Amino Acid matrix (or Amino Acid properties matrix)
     LDH.amino.gapless=remove_gaps_groups(LDH.amino,LDH.groups)
     #Add Psuedo counts
     LDH.pseudo=LDH.amino.gapless+1

     LDH.binary.bga=bga(t(LDH.pseudo),LDH.groups)
     plot(LDH.binary.bga)

