aa.comp()

Description

Returns a table with the amino acid composition of the target protein

Usage

aa.comp(target, uniprot = TRUE)

Arguments

target a character string specifying the UniProt ID of the protein of interest or, alternatively, the sequence of that protein.

uniprot logical, if TRUE the argument ‘target’ should be an ID.

Value

Returns a dataframe with the absolute frequency of each type of residue found in the target peptide.

See Also

aa.at(), is.at(), renum.pdb(), renum.meto(), renum()

Details

The ptm package offers a set of ancillary functions aimed to carry out rutinary work, which may be needed when more elaborated analysis are required. Among these ancillary function are:

• aa.at
• is.at
• aa.comp (the current document)
• renum.pdb
• renum.meto
• renum

The function aa.comp() provides us the amino acid composition of a given sequence.

library(knitr)
mytable <- aa.comp('P01009')
mytable$percent <- round(100 * mytable$frequency/sum(mytable$frequency), 1)                
kable(mytable)

Above we have passed the UniProt ID of the protein of interest, but we can also provide any customized sequence:

library(knitr)
mytable <- aa.comp('MAARESAPFDR', uniprot = FALSE)
mytable$percent <- round(100 * mytable$frequency/sum(mytable$frequency), 1)                
kable(mytable)