bgafun: BGAfun A method to identify specifity determining residues in protein families

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

Author
Iain Wallace
Date of publication
None
Maintainer
Iain Wallace <iain.wallace@ucd.ie>
License
Artistic-2.0
Version
1.36.0

View on Bioconductor

Man pages

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...

Files in this package

bgafun/DESCRIPTION
bgafun/NAMESPACE
bgafun/R
bgafun/R/Calculate_Row_Weights.R
bgafun/R/Henikoff_weights.R
bgafun/R/Weight_Amino.R
bgafun/R/add_pseudo_counts.R
bgafun/R/amino_counts.R
bgafun/R/average_cols_aap.R
bgafun/R/calculate_pseudo.R
bgafun/R/convert_aln_AAP.R
bgafun/R/convert_aln_amino.R
bgafun/R/convert_seq_AAP.R
bgafun/R/convert_seq_amino.R
bgafun/R/create_colnames_AAP.R
bgafun/R/create_colnames_amino.R
bgafun/R/create_probab.R
bgafun/R/create_profile.R
bgafun/R/create_profile_strings.R
bgafun/R/pseudo_counts.R
bgafun/R/remove_gaps.R
bgafun/R/remove_gaps_groups.R
bgafun/R/run_between_pca.R
bgafun/R/sum_20_aln.R
bgafun/R/sum_20_cols.R
bgafun/R/sum_aln.R
bgafun/R/top_residues_2_groups.R
bgafun/build
bgafun/build/vignette.rds
bgafun/data
bgafun/data/LDH.aap.ave.rda
bgafun/data/LDH.aap.rda
bgafun/data/LDH.amino.gapless.rda
bgafun/data/LDH.amino.pseudo.rda
bgafun/data/LDH.amino.rda
bgafun/data/LDH.groups.rda
bgafun/data/LDH.rda
bgafun/inst
bgafun/inst/doc
bgafun/inst/doc/bgafun.R
bgafun/inst/doc/bgafun.pdf
bgafun/inst/doc/bgafun.rnw
bgafun/inst/sequences
bgafun/inst/sequences/LDH-MDH-PF00056.fasta
bgafun/man
bgafun/man/Calculate_Row_Weights.Rd
bgafun/man/Henikoff_weights.Rd
bgafun/man/LDH.Rd
bgafun/man/LDH.aap.Rd
bgafun/man/LDH.aap.ave.Rd
bgafun/man/LDH.amino.Rd
bgafun/man/LDH.amino.gapless.Rd
bgafun/man/LDH.amino.pseudo.Rd
bgafun/man/LDH.groups.Rd
bgafun/man/Weight_Amino.Rd
bgafun/man/add_pseudo_counts.Rd
bgafun/man/amino_counts.Rd
bgafun/man/average_cols_aap.Rd
bgafun/man/bgafun.Rd
bgafun/man/calculate_pseudo.Rd
bgafun/man/convertAAP.package.Rd
bgafun/man/convert_aln_AAP.Rd
bgafun/man/convert_aln_amino.Rd
bgafun/man/convert_amino.package.Rd
bgafun/man/convert_seq_AAP.Rd
bgafun/man/convert_seq_amino.Rd
bgafun/man/create_colnames_AAP.Rd
bgafun/man/create_colnames_amino.Rd
bgafun/man/create_probab.Rd
bgafun/man/create_profile.Rd
bgafun/man/create_profile_strings.Rd
bgafun/man/pseudo_counts.Rd
bgafun/man/remove_gaps.Rd
bgafun/man/remove_gaps_groups.Rd
bgafun/man/run_between_pca.Rd
bgafun/man/sum_20_aln.Rd
bgafun/man/sum_20_cols.Rd
bgafun/man/sum_aln.Rd
bgafun/man/top_residues_2_groups.Rd
bgafun/vignettes
bgafun/vignettes/Bibtext.bib
bgafun/vignettes/bgafun.rnw
bgafun/vignettes/mystyle.bst