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Annotate sites according to a dataframe containing annotation

Source: R/site_annotation.R
annotate_site.Rd

Annotate sites of interest by giving them a custom name. Some analyses and plots can be applied on these specific sites when only_annotated parameter is available.

Usage

annotate_site(ribo, annot, anno_rna = 2, anno_pos = 1, anno_value = 3)

Arguments

ribo

a RiboClass object to annotate, see : load_ribodata

annot

The dataframe containing annotations.

anno_rna

Name or index of the column in annot containing RNAs' name.

anno_pos

Name or index of the column in annot containing site position inside RNA.

anno_value

Name or index of the column in annot containing nomenclature to apply.

Value

An annotated RiboClass (the site column in data should be filled with names from annot_value for known position).

Details

This function will fill the 'site' column in your RiboClass's data with a nomenclature given in annot.

Examples

data('ribo_toy')
data('human_methylated')
ribo_toy <- rename_rna(ribo_toy ,c('5S','5.8S','18S','28S'))
ribo_toy <- annotate_site(ribo_toy,human_methylated,anno_value ='Nomenclature')