imprints_isoform_peptides: imprints_isoform_peptides

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

imprints_isoform_peptides

Description

Function to check if the hits found by imprints_cleaved_peptides could be due to alternate splicing forms being more expressed and not due to protein cleavage.

Usage

imprints_isoform_peptides(
  data,
  data_cleaved,
  control,
  fasta,
  minimum_align = 5,
  save_xlsx = TRUE,
  xlsxname = "RESP_isoform_mapping"
)

Arguments

data	The normalized peptides data set, i.e. the outpout from imprints_normalize_peptides.
data_cleaved	The cleavage hits data set, i.e. the outpout from imprints_cleaved_peptides.
control	The control treatment from your dataset.
fasta	The path to the FASTA file you used for the search
minimum_align	Numeric to tell the minimum aligned sequence length. Default to 5. It is advised to put the same as the minimum peptide sequence length you selected in the proteomics search software you used.
save_xlsx	Logical to tell if you want to save the categorized hits in an xlsx file. Default to TRUE.
xlsxname	The name of your saved file.

Details

When a hit is returned by imprints_cleaved_peptides, it means that this protein has a peptide position where the IMPRINTS profiles of the two obtained parts are significantly different. This difference can be caused by protein modification and mainly proteolysis; but if a splicing form of protein is more expressed than its canonical form, a significant difference in the profiles can also occur. The aim here is to refilter the hit list and give the possible splicing forms which could be more expressed based on the output of imprints_cleaved_peptides and the sequence alignments of the isoform sequence and its corresponding canonical form.

Value

A dataframe containing the potential splicing forms which could be more expressed instead of the protein being cleaved

See Also

imprints_cleaved_peptides

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