Generating Utility {cubfits} | R Documentation |
These utility functions generate and summarize sequence strings into several
useful formats such as reu13.df
, y
, and
n
, etc.
gen.reu13.df(seq.string, phi.df = NULL, aa.names = .CF.GV$amino.acid, split.S = TRUE, drop.X = TRUE, drop.MW = TRUE, drop.1st.codon = TRUE) gen.y(seq.string, aa.names = .CF.GV$amino.acid, split.S = TRUE, drop.X = TRUE, drop.MW = TRUE) gen.n(seq.string, aa.names = .CF.GV$amino.acid, split.S = TRUE, drop.X = TRUE, drop.MW = TRUE) gen.reu13.list(seq.string, aa.names = .CF.GV$amino.acid, split.S = TRUE, drop.X = TRUE, drop.MW = TRUE, drop.1st.codon = TRUE) gen.phi.Obs(phi.df) gen.scuo(seq.string, aa.names = .CF.GV$amino.acid, split.S = TRUE, drop.X = TRUE, drop.MW = TRUE)
seq.string |
a list of sequence strings. |
phi.df |
a |
aa.names |
a vector contains amino acid names for analysis. |
split.S |
split amino acid 'S' if any. |
drop.X |
drop amino acid 'X' if any. |
drop.MW |
drop amino acid 'M' and 'W' if any. |
drop.1st.codon |
if drop the first codon. |
These functions mainly take inputs of sequence strings
seq.string
or phi.df
and turn them
into corresponding format.
The outputs are data structure in corresponding formats. See AllDataFormats for details.
Wei-Chen Chen wccsnow@gmail.com.
https://github.com/snoweye/cubfits/
AllDataFormats,
read.seq()
, read.phi.df()
, and
convert.seq.data.to.string()
.
## Not run: suppressMessages(library(cubfits, quietly = TRUE)) seq.data <- read.seq(get.expath("seq_200.fasta")) phi.df <- read.phi.df(get.expath("phi_200.tsv")) aa.names <- c("A", "C", "D") # Read in from FASTA file. seq.string <- convert.seq.data.to.string(seq.data) reu13.df <- gen.reu13.df(seq.string, phi.df, aa.names) reu13.list.new <- gen.reu13.list(seq.string, aa.names) y <- gen.y(seq.string, aa.names) n <- gen.n(seq.string, aa.names) scuo <- gen.scuo(seq.string, aa.names) # Convert to list format. reu13.list <- convert.reu13.df.to.list(reu13.df) y.list <- convert.y.to.list(y) n.list <- convert.n.to.list(n) ## End(Not run)