multiple_modifications: A function to generate a list of properly formatted proforma...

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

A function to generate a list of properly formatted proforma strings

Description

A function to generate a list of properly formatted proforma strings

Usage

multiple_modifications(
  Sequence,
  Modification,
  ReturnUnmodified = FALSE,
  AlternativeGlossary = NULL
)

Arguments

Sequence	A valid protein sequence. It may start with "M." which gets removed. Required.
Modification	An IsoForma modifications annotation written as "PTM,Residue(Positions)[Number of Modifications]". Required.
ReturnUnmodified	A TRUE/FALSE to indicate whether the unmodified sequence should be returned with the list or not. Default is FALSE.
AlternativeGlossary	Try a different glossary. See system.file("extdata", "Unimod_v20220602.csv", package = "pspecterlib) for formatting.

Examples

## Not run: 

# Single modification of a single PTM examples 
multiple_modifications("TRICITIES", "Methyl,(3)[1]")
multiple_modifications("TRICITIES", "1.00727,(3,5,7)[1]")

# Multiple modifications of a single PTM example
multiple_modifications("TRICITIES", "Methyl,(3,5,7)[2]") 

# Multiple modifications with a fixed position
multiple_modifications("TRICITIES", "Methyl,(3^,5,7)[2]") 

# Multiple modifications with two fixed positions 
multiple_modifications("TRICITIES", "Methyl,(3^,5,7^)[2]")

# Multiple modifications of a single PTM with any "X" residue
multiple_modifications("TRICITIES", "Methyl,(1,2,3,4,5,6,7,8,9)[2]")

# Multiple modifications with multiple PTMs examples and the base sequence returned
multiple_modifications("TRICITIES", "Methyl,(1)[1];Acetyl,(2,4,9)[1]", ReturnUnmodified = TRUE)
multiple_modifications("TRICITIES", "Methyl,(1,2,3,4,5,6,7,8,9)[1];Acetyl,(2,4,9)[1]", ReturnUnmodified = TRUE)
multiple_modifications("TRICITIES", "Methyl,(1^,2,3,4,5,6,7^,8,9)[3];1.00727,(2,4,9)[1]", ReturnUnmodified = TRUE)


## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.