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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bgafun")
AuthorIain Wallace
Bioconductor views Classification
Date of publicationNone
MaintainerIain Wallace <iain.wallace@ucd.ie>
LicenseArtistic-2.0
Version1.38.0

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

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

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