get_aa_transition_matrix: Get an amino acid transition matrix
In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question
View source: R/get_aa_transition_matrix.R
get_aa_transition_matrix R Documentation
Get an amino acid transition matrix
Description
From Dang, Cuong Cao, et al. "FLU, an amino acid substitution model for
influenza proteins." BMC evolutionary biology 10.1 (2010): 99.
Usage
get_aa_transition_matrix(transition_matrix_name)
Arguments
transition_matrix_name
the name of an amino acid transition matrix,
for example, BLOSUM62
Details
File downloaded from
ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU/Flu_All_it2.txt_PAML.txt
As can be seen in https://github.com/stephaneguindon/phyml/blob/master/src/io.c#L3188, the column names are Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu
Lys Met Phe Pro Ser Thr Trp Tyr Val
Value
a tibble, with column names equal to the uppercase
amino acid name
Author(s)
Richèl J.C. Bilderbeek
richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.
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View source: R/get_aa_transition_matrix.R
| get_aa_transition_matrix | R Documentation |
Get an amino acid transition matrix
Description
From Dang, Cuong Cao, et al. "FLU, an amino acid substitution model for influenza proteins." BMC evolutionary biology 10.1 (2010): 99.
Usage
get_aa_transition_matrix(transition_matrix_name)
Arguments
transition_matrix_name |
the name of an amino acid transition matrix,
for example, |
Details
File downloaded from
ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU/Flu_All_it2.txt_PAML.txt
As can be seen in https://github.com/stephaneguindon/phyml/blob/master/src/io.c#L3188, the column names are Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu
Lys Met Phe Pro Ser Thr Trp Tyr Val
Value
a tibble, with column names equal to the uppercase amino acid name
Author(s)
Richèl J.C. Bilderbeek
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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