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

AuthorIain Wallace
Date of publicationNone
MaintainerIain Wallace <iain.wallace@ucd.ie>
LicenseArtistic-2.0
Version1.36.0

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...

Functions

add_pseudo_counts Man page
amino_counts Man page
average_cols_aap Man page
bgafun Man page
calculate_pseudo Man page
Calculate_Row_Weights Man page
convertAAP Man page
convertAAP-package Man page
convert_aln_AAP Man page
convert_aln_amino Man page
convert_amino-package Man page
convert_seq_AAP Man page
convert_seq_amino Man page
create_colnames_AAP Man page
create_colnames_amino Man page
create_probab Man page
create_profile Man page
create_profile_strings Man page
Henikoff_weights Man page
LDH Man page
LDH.aap Man page
LDH.aap.ave Man page
LDH.amino Man page
LDH.amino.gapless Man page
LDH.amino.pseudo Man page
LDH.groups Man page
pseudo_counts Man page
remove_gaps Man page
remove_gaps_groups Man page
run_between_pca Man page
sum_20_aln Man page
sum_20_cols Man page
sum_aln Man page
top_residues_2_groups Man page
Weight_Amino Man page

Files

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

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