Description Usage Arguments Details Value Warning Author(s) See Also
This will read in a file of sequences and create a Sequences-class object.
1 2 3 | read.sequences(file, header = FALSE, sep = "",
quote = "\"", dec = ".", fill = FALSE,
comment.char = "", alphabet = aabet)
|
file |
the name of the file which the data are to be read from.
Each row of the table appears as one line of the file. If it
does not contain an _absolute_ path, the file name is
_relative_ to the current working directory, Alternatively,
|
header |
a logical value indicating whether the file contains the
names of the variables as its first line. If missing, the
value is determined from the file format: |
sep |
the field separator character. Values on each line of the
file are separated by this character. If |
quote |
the set of quoting characters. To disable quoting altogether,
use |
dec |
the character used in the file for decimal points. |
fill |
logical. If |
comment.char |
character: a character vector of length one containing a
single character or an empty string. Use |
alphabet |
The alphabet to use for the sequences. The default alphabet contains
the canonical 20 amino acids, as well as B, Z, X, and |
See the details for read.table
for more information about
reading the file. The file format should be one sequence per line with
no spaces between the residues. Note that your file could contain
additional columns with experimental data, but the first column must
contain the sequences. For example:
————————
Sequences Response
GFF- 1.0
RGD- 0.85
GRFD 10.1
-GFR 0.1
FGRD 5.2
——————
Each sequence should be the same length, thus
-
should be use to pad the sequences, as seen in the example. Use an alignment
algorithm, such as Clustal, to align your sequences before reading.
An object of class Sequences
. This is a small
extension of the matrix class, and as expected, each row of the matrix
corresponds to a single sequence. The sequences are always represented
as integers. The rownames of the matrix are the original string/character
representations of the sequences.
As mentioned above, it is important to align your sequences before reading if they are of differing lengths. For example, use the online ClustalW2 algorithm available from the European Bioinformatics Institutes's website.
Andrew White
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