imprints_sequence_peptides: imprints_sequence_peptides

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

imprints_sequence_peptides

Description

Function to select proteins and sequence from peptide data, sum up the peptide that are not selected (before and after the sequence selected) and then plot the fold change on a pdf.

Usage

imprints_sequence_peptides(
  data,
  proteins = NULL,
  sequence = NULL,
  control = "Vehicle",
  margin = 2,
  barplot = FALSE,
  dataset_name = "imprints"
)

Arguments

data	The input data set, the peptide data file filtered (non TMT modification removed) and non log2 transformed.
proteins	The proteins you want to select. If NULL, select all.
sequence	The peptide position you want to select. It needs to be a list that contains the same number of element than the number of proteins or only one element. An element can be a string like 191-199 or a vector that contains several strings like c("52-71", "207-222"). Anyway, it needs to be in the format number-number. If it's NULL, it will only select according the proteins so you can plot all the peptides from those.
control	The condition corresponding to the control in your dataset.
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.
barplot	Logical to tell if you want to plot the barplots from the obtained fold-changes. Default is FALSE
dataset_name	The name of your dataset to save your file.

Value

The caldiff output from the peptide position from the protein you selected; save it and also save the barplots.

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