This function reads protein sequences in FASTA format.
readFASTA(
file = system.file("protseq/P00750.fasta", package = "protr"),
legacy.mode = TRUE,
seqonly = FALSE
)
Character vector of the protein sequences.
The three returned argument are just different forms of the same output. If one is interested in a Mahalanobis metric over the original data space, the first argument is all she/he needs. If a transformation into another space (where one can use the Euclidean metric) is preferred, the second returned argument is sufficient. Using A and B is equivalent in the following sense.
Path to the file containing the protein sequences
in FASTA format. If it does not contain an absolute or
relative path, the file name is relative to the current
working directory, getwd
.
The default here is to read the P00750.fasta
file which
is present in the protseq
directory of the protr package.
If set to TRUE
, lines starting with a
semicolon (;
) are ignored. Default value is TRUE
.
If set to TRUE
, only sequences as returned
without attempt to modify them or to get their names and
annotations (execution time is divided approximately
by a factor 3). Default value is FALSE
.
Nan Xiao <https://nanx.me>
Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85: 2444--2448.
See getUniProt
for retrieving
protein sequences from uniprot.org.
P00750 <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))
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