Calculate_Row_Weights
(Package: bgafun) :
Calculate the sequence weights for all the rows in my amino,using label as the grouping
This will calculate the sequence weights for each group using the Heinkoff and Heinkoff method. Each residue in the sequence is assigned a weight depending on how unique it is in the column. The sequence weight is then the sum of these weights, and the total weight is the number of groups
● Data Source:
BioConductor
● Keywords: manip
● Alias: Calculate_Row_Weights
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Henikoff_weights
(Package: bgafun) :
Calculates Henikoff weights for each sequence in a binary amino acid matrix
Internal Function Calculates a sequence weight for each sequence in an alignment using the Henikoff method.
● Data Source:
BioConductor
● Keywords: manip
● Alias: Henikoff_weights
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LDH
(Package: bgafun) :
LDH alignment read in from a file
Seqinr representation of the LDH example alignment.
● Data Source:
BioConductor
● Keywords: IO
● Alias: LDH
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Weight_Amino
(Package: bgafun) :
Calculates sequence weight for each sequence in an amino acid matrix
Internal Function Calculates sequence weight for each sequence, and multiples the matrix by this weight. It returns a weighted amino acid matrix.
● Data Source:
BioConductor
● Keywords: manip
● Alias: Weight_Amino
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add_pseudo_counts
(Package: bgafun) :
Add pseudo counts to amino acid matrix based on defined groups
This function will add pseudo counts to binary amino acid matrix based on the defined groups. It is used to minimise the effect of small sample size. The method of Henikoff and Henikoff is used to calculate the pseudocounts An alternative method is to simply add 1 to the binary matrix
● Data Source:
BioConductor
● Keywords: manip
● Alias: add_pseudo_counts
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amino_counts
(Package: bgafun) :
calculate count of amino acid types at each position
Internal Function Calculate the counts of amino acid types at each position in an alignment from a binary amino acid matrix
● Data Source:
BioConductor
● Keywords: manip
● Alias: amino_counts
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average_cols_aap
(Package: bgafun) :
Replaces gaps with the average of the column
This function will deal with gaps in the Amino Acid Property encoding scheme It replaces gaps with the average in the column for each group, provided the column is highly occupied for that group. It will only average out over columns that have high percentage of gaps It will remove all other columns containing gaps.
● Data Source:
BioConductor
● Keywords: IO
● Alias: average_cols_aap
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This Package combines between group analysis with sequence alignments to identify specifity determining residues in protein families
● Data Source:
BioConductor
● Keywords: package
● Alias: bgafun
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calculate_pseudo
(Package: bgafun) :
Calculates pseudo count for each column in the amino acid matrix
Internal function Calculates the pseudo count for each column in the amino acid matrix
● Data Source:
BioConductor
● Keywords: manip
● Alias: calculate_pseudo
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Convert an alignment read in by seqinr into a matrix using the AAP encoding. this is suitable for BGA analysis using PCA
● Data Source:
BioConductor
● Keywords: package
● Alias: convertAAP, convertAAP-package
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