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bgafun (version 1.34.0)

BGAfun A method to identify specifity determining residues in protein families

Description

A method to identify specifity determining residues in protein families using Between Group Analysis

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Version

Version

1.34.0

License

Artistic-2.0

Maintainer

Iain Wallace

Last Published

February 15th, 2017

Functions in bgafun (1.34.0)

convert_aln_amino

Converts an alignment object into binary amino matrix
LDH.amino.gapless

Amino acid matrix after removing gaps
convert_aln_AAP

Converts alignment into a matrix using the amino acid property encoding
sum_aln

Calculate number of amino acids in each position in an alignment
LDH.amino

Binary amino acid matrix after converting the Lactate alignment
create_colnames_amino

Creates the column names for the binary matrix
Calculate_Row_Weights

Calculate the sequence weights for all the rows in my amino,using label as the grouping
create_profile

Creates a sequence profile for an binary amino acid matrix
LDH.groups

Groups in the LDH alignment
calculate_pseudo

Calculates pseudo count for each column in the amino acid matrix
convertAAP-package

Converts an alignment into a matrix using the AAP encoding
run_between_pca

run PCA to identify functional positions in an alignment
create_probab

Generates probability matrix for pseudocounts calculation
amino_counts

calculate count of amino acid types at each position
Weight_Amino

Calculates sequence weight for each sequence in an amino acid matrix
top_residues_2_groups

Return a list of the top residues at either end of the axis
add_pseudo_counts

Add pseudo counts to amino acid matrix based on defined groups
BGAfun

BGAfun A method to identify specifity determining residues in protein families
LDH

LDH alignment read in from a file
sum_20_aln

Calculates number of amino acids in each group of 20 columns (1 column in an alignment)
remove_gaps

Removes gaps from a amino binary matrix
create_colnames_AAP

Create column names for an AAP matrix
pseudo_counts

Calculate pseudo counts for a profile
remove_gaps_groups

remove gaps from a binary amino matrix
LDH.aap.ave

AAP matrix
LDH.amino.pseudo

Amino acid matrix after adding pseudo counts
average_cols_aap

Replaces gaps with the average of the column
convert_amino-package

The functions required to convert an alignment into a binary matrix suitable for BGA analysis
sum_20_cols

Calculate number of amino acids in a column of an alignment
LDH.aap

AAP matrix
Henikoff_weights

Calculates Henikoff weights for each sequence in a binary amino acid matrix
convert_seq_AAP

Convert sequence into string representing AAP values
convert_seq_amino

Converts a single seqeunce into a binary string
create_profile_strings

Create a profile string for each group in an alignment