imprints_remove_peptides: imprints_remove_peptides

In mgerault/mineCETSAapp: A shiny app for IMPRINTS.CETSA package

imprints_remove_peptides

Description

Function to filter some peptides according there sequence. For example after using imprints_sequence_peptides, if you want to remove the peptides which corresponds to the cleaved sites.

Usage

imprints_remove_peptides(
  data,
  proteins = NULL,
  sequence,
  margin = 2,
  mode = c("remove", "keep")
)

Arguments

data	A peptides dataset, typically after imprints_sequence_peptides. It needs to contains the columns 'Master Protein Accessions' and 'Positions in Master Proteins'.
proteins	The proteins from which you want to remove/keep the peptides. If NULL and you put one sequence, it will remove/keep all these peptides for all proteins from peptides data. If NULL and you put several sequence, the number of sequence you put needs to match the number of proteins you have in your peptides data.
sequence	The peptide position you want to remove/keep. If you put one sequence, it will remove/keep it for all proteins from your peptides data; otherwise it needs to match the number of proteins you put or have in your dataset. The format needs to be a number followed by a dash and another number, like this : '208-221'.
margin	Numeric to tell the margin number of amino acid added to the sequences selected. This avoid peptide selection ambigutiy when a peptide has only a small number of amino acid more than the sequence selected. Default is set to 2.
mode	Character to specify if you want to remove or only the peptides selected; either 'remove' or 'keep'. Default is 'remove'.

Value

Your filtered dataset

mgerault/mineCETSAapp documentation built on April 17, 2025, 7:24 p.m.