R: Count sequence patterns

countPatterns {alakazam} | R Documentation

## Count sequence patterns

### Description

`countPatterns` counts the fraction of times a set of character patterns occur in a set of sequences.

### Usage

    countPatterns(seq, patterns, nt = FALSE, trim = FALSE,
      label = "REGION")

### Arguments

`seq` | character vector of either DNA or amino acid sequences.
`patterns` | list of sequence patterns to count in each sequence. If the list is named, then names will be assigned as the column names of output data.frame.
`nt` | if `TRUE` then `seq` are DNA sequences and and will be translated before performing the pattern search.
`trim` | if `TRUE` remove the first and last codon or amino acid from each sequence before the pattern search. If `FALSE` do not modify the input sequences.
`label` | string defining a label to add as a prefix to the output column names.

### Value

A data.frame containing the fraction of times each sequence pattern was found.

### Examples

    seq <- c("TGTCAACAGGCTAACAGTTTCCGGACGTTC",
             "TGTCAGCAATATTATATTGCTCCCTTCACTTTC",
             "TGTCAAAAGTATAACAGTGCCCCCTGGACGTTC")
    patterns <- c("A", "V", "[LI]")
    names(patterns) <- c("ARG", "VAL", "ISO_LEU")
    countPatterns(seq, patterns, nt=TRUE, trim=TRUE, label="CDR3")

[Package alakazam version 0.3.0 Index]