Man pages for bgafun
BGAfun A method to identify specifity determining residues in protein families
| add_pseudo_counts | Add pseudo counts to amino acid matrix based on defined... |
| amino_counts | calculate count of amino acid types at each position |
| average_cols_aap | Replaces gaps with the average of the column |
| bgafun | BGAfun A method to identify specifity determining residues in... |
| calculate_pseudo | Calculates pseudo count for each column in the amino acid... |
| Calculate_Row_Weights | Calculate the sequence weights for all the rows in my... |
| convertAAP.package | Converts an alignment into a matrix using the AAP encoding |
| convert_aln_AAP | Converts alignment into a matrix using the amino acid... |
| convert_aln_amino | Converts an alignment object into binary amino matrix |
| convert_amino.package | The functions required to convert an alignment into a binary... |
| convert_seq_AAP | Convert sequence into string representing AAP values |
| convert_seq_amino | Converts a single seqeunce into a binary string |
| create_colnames_AAP | Create column names for an AAP matrix |
| create_colnames_amino | Creates the column names for the binary matrix |
| create_probab | Generates probability matrix for pseudocounts calculation |
| create_profile | Creates a sequence profile for an binary amino acid matrix |
| create_profile_strings | Create a profile string for each group in an alignment |
| Henikoff_weights | Calculates Henikoff weights for each sequence in a binary... |
| LDH | LDH alignment read in from a file |
| LDH.aap | AAP matrix |
| LDH.aap.ave | AAP matrix |
| LDH.amino | Binary amino acid matrix after converting the Lactate... |
| LDH.amino.gapless | Amino acid matrix after removing gaps |
| LDH.amino.pseudo | Amino acid matrix after adding pseudo counts |
| LDH.groups | Groups in the LDH alignment |
| pseudo_counts | Calculate pseudo counts for a profile |
| remove_gaps | Removes gaps from a amino binary matrix |
| remove_gaps_groups | remove gaps from a binary amino matrix |
| run_between_pca | run PCA to identify functional positions in an alignment |
| sum_20_aln | Calculates number of amino acids in each group of 20 columns... |
| sum_20_cols | Calculate number of amino acids in a column of an alignment |
| sum_aln | Calculate number of amino acids in each position in an... |
| top_residues_2_groups | Return a list of the top residues at either end of the axis |
| Weight_Amino | Calculates sequence weight for each sequence in an amino acid... |
