sanitizeInput {Modstrings} | R Documentation

## Sanitize input strings for use with ModString classes

### Description

Since the one letter nomenclature for RNA and DNA modification differs depending on the source, a translation to a common alphabet is necessary.

`sanitizeInput` exchanges based on a dictionary. The dictionary is expected to be a `DataFrame` with two columns, `mods_abbrev` and `short_name`. Based on the `short_name` the characters from in the input are converted from values of `mods_abbrev` into the the ones from `alphabet`.

Only different values will be searched for and exchanged.

`sanitizeFromModomics` and `sanitizeFromtRNAdb` use a predefined dictionary, which is builtin.

### Usage

    sanitizeInput(input, dictionary)

    sanitizeFromModomics(input)

    sanitizeFromtRNAdb(input)

### Arguments

`input` | a `character` vector, which should be converted
`dictionary` | a DataFrame containing at least two columns `mods_abbrev` and `short_name`. From this a dictionary table is contructed for exchaning old to new letters.

### Value

the modified `character` vector compatible for constructing a `ModString` object.

### Examples

    # Modomics
    chr <- "AGC@"
    # Error since the @ is not in the alphabet
    ## Not run:
    seq <- ModRNAString(chr)

    ## End(Not run)
    seq <- ModRNAString(sanitizeFromModomics(chr))

    # tRNAdb
    chr <- "AGC+"
    # No error but the + has a different meaning in the alphabet
    ## Not run:
    seq <- ModRNAString(chr)

    ## End(Not run)
    seq <- ModRNAString(sanitizeFromtRNAdb(chr))

[Package Modstrings version 1.6.0 Index]