BGAfun A method to identify specifity determining residues in protein families


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Documentation for package ‘bgafun’ version 1.14.0

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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