Generating Utility {cubfits} | R Documentation |
Generating Data Structure
Description
These utility functions generate and summarize sequence strings into several
useful formats such as reu13.df
, y
, and
n
, etc.
Usage
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)
Arguments
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. |
Details
These functions mainly take inputs of sequence strings
seq.string
or phi.df
and turn them
into corresponding format.
Value
The outputs are data structure in corresponding formats. See AllDataFormats for details.
Author(s)
Wei-Chen Chen wccsnow@gmail.com.
References
https://github.com/snoweye/cubfits/
See Also
AllDataFormats,
read.seq()
, read.phi.df()
, and
convert.seq.data.to.string()
.
Examples
## 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)
[Package cubfits version 0.1-4 Index]