Man pages for Bioconductor-mirror/bgafun
BGAfun A method to identify specifity determining residues in protein families

add_pseudo_countsAdd pseudo counts to amino acid matrix based on defined...
amino_countscalculate count of amino acid types at each position
average_cols_aapReplaces gaps with the average of the column
bgafunBGAfun A method to identify specifity determining residues in...
calculate_pseudoCalculates pseudo count for each column in the amino acid...
Calculate_Row_WeightsCalculate the sequence weights for all the rows in my...
convertAAP.packageConverts an alignment into a matrix using the AAP encoding
convert_aln_AAPConverts alignment into a matrix using the amino acid...
convert_aln_aminoConverts an alignment object into binary amino matrix
convert_amino.packageThe functions required to convert an alignment into a binary...
convert_seq_AAPConvert sequence into string representing AAP values
convert_seq_aminoConverts a single seqeunce into a binary string
create_colnames_AAPCreate column names for an AAP matrix
create_colnames_aminoCreates the column names for the binary matrix
create_probabGenerates probability matrix for pseudocounts calculation
create_profileCreates a sequence profile for an binary amino acid matrix
create_profile_stringsCreate a profile string for each group in an alignment
Henikoff_weightsCalculates Henikoff weights for each sequence in a binary...
LDHLDH alignment read in from a file
LDH.aapAAP matrix
LDH.aap.aveAAP matrix
LDH.aminoBinary amino acid matrix after converting the Lactate...
LDH.amino.gaplessAmino acid matrix after removing gaps
LDH.amino.pseudoAmino acid matrix after adding pseudo counts
LDH.groupsGroups in the LDH alignment
pseudo_countsCalculate pseudo counts for a profile
remove_gapsRemoves gaps from a amino binary matrix
remove_gaps_groupsremove gaps from a binary amino matrix
run_between_pcarun PCA to identify functional positions in an alignment
sum_20_alnCalculates number of amino acids in each group of 20 columns...
sum_20_colsCalculate number of amino acids in a column of an alignment
sum_alnCalculate number of amino acids in each position in an...
top_residues_2_groupsReturn a list of the top residues at either end of the axis
Weight_AminoCalculates sequence weight for each sequence in an amino acid...
Bioconductor-mirror/bgafun documentation built on June 1, 2017, 4:25 a.m.