R: Calculates the average polarity of amino acid sequences

polar {alakazam} | R Documentation

## Calculates the average polarity of amino acid sequences

### Description

`polar` calculates the average polarity score of amino acid sequences. Non-informative positions are excluded, where non-informative is defined as any character in `c("X", "-", ".", "*")`.

### Usage

    polar(seq, polarity = NULL)

### Arguments

`seq` | vector of strings containing amino acid sequences.
`polarity` | named numerical vector defining polarity scores for each amino acid, where names are single-letter amino acid character codes. If `NULL`, then the Grantham, 1974 scale is used.

### Value

A vector of bulkiness scores for the sequence(s).

### References

1. Grantham R. Amino acid difference formula to help explain protein evolution. Science 185, 862-864 (1974).

### See Also

For additional size related indices see `aaindex`.

### Examples

    # Default scale
    seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT")
    polar(seq)

    # Use the Zimmerman et al, 1968 polarity scale from the seqinr package
    library(seqinr)
    data(aaindex)
    x <- aaindex[["ZIMJ680103"]]$I
    # Rename the score vector to use single-letter codes
    names(x) <- translateStrings(names(x), ABBREV_AA)
    # Calculate polarity
    polar(seq, polarity=x)

[Package alakazam version 0.3.0 Index]