read.sequences: Read sequence file
In peplib: Peptide Library Analysis Methods

Description Usage Arguments Details Value Warning Author(s) See Also

This will read in a file of sequences and create a Sequences-class object.

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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, `getwd()`. Tilde-expansion is performed where supported. As from R 2.10.0 this can be a compressed file (see `file`). Alternatively, `file` can be a readable text-mode `connection` (which will be opened for reading if necessary, and if so `close`d (and hence destroyed) at the end of the function call). (If `stdin()` is used, the prompts for lines may be somewhat confusing. Terminate input with a blank line or an EOF signal, `Ctrl-D` on Unix and `Ctrl-Z` on Windows. Any pushback on `stdin()` will be cleared before return.) `file` can also be a complete URL.
`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: `header` is set to `TRUE` if and only if the first row contains one fewer field than the number of columns.
`sep`	the field separator character. Values on each line of the file are separated by this character. If `sep = ""` (the default for `read.table`) the separator is `white space`, that is one or more spaces, tabs, newlines or carriage returns.
`quote`	the set of quoting characters. To disable quoting altogether, use `quote = ""`. See `scan` for the behavior on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless `colClasses` is specified.
`dec`	the character used in the file for decimal points.
`fill`	logical. If `TRUE` then in case the rows have unequal length, blank fields are implicitly added.
`comment.char`	character: a character vector of length one containing a single character or an empty string. Use `""` to turn off the interpretation of comments altogether.
`alphabet`	The alphabet to use for the sequences. The default alphabet contains the canonical 20 amino acids, as well as B, Z, X, and `-`, where X is an unspecified residue and `-` is a gap.

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:

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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

Sequences, read.fasta

peplib documentation built on May 29, 2017, 10:52 p.m.