convertAAP-package |
Converts an alignment into a matrix using the AAP encoding |
convert_amino-package |
The functions required to convert an alignment into a binary matrix suitable for BGA analysis |
add_pseudo_counts |
Add pseudo counts to amino acid matrix based on defined groups |
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 protein families |
calculate_pseudo |
Calculates pseudo count for each column in the amino acid matrix |
Calculate_Row_Weights |
Calculate the sequence weights for all the rows in my amino,using label as the grouping |
convertAAP |
Converts an alignment into a matrix using the AAP encoding |
convert_aln_AAP |
Converts alignment into a matrix using the amino acid property encoding |
convert_aln_amino |
Converts an alignment object into binary amino matrix |
convert_seq_amino |
Converts a single seqeunce into a binary string |
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 amino acid matrix |
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 alignment |
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 (1 column in an alignment) |
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 alignment |
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 matrix |