imprints_cleaved_peptides: imprints_cleaved_peptides

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

imprints_cleaved_peptides

Description

Function to find proteins that are potentially cleaved and their cleaved sites. For more information, see Details section.

Usage

imprints_cleaved_peptides(
  data,
  data_diff = NULL,
  control = "Vehicle",
  min_ValidValue = 0.4,
  min_peptide = 4,
  FDR = 0.01,
  comb_pv_method = c("george", "fisher", "edgington"),
  RESP_score = 0.5,
  fixed_score_cutoff = FALSE,
  categorize = TRUE,
  curvature = 0.05,
  folder_name = ""
)

Arguments

data	The normalized peptides data set, i.e. the outpout from imprints_normalize_peptides.
data_diff	The log2 fold-changes peptides data set, i.e. the outpout from imprints_sequence_peptides. If NULL, it will be computed.
control	The control treatment from your dataset.
min_ValidValue	The minimum proportion of non-missing values per peptides. Default is 0.4; so if 6 temperatures need at least 3 non missing values.
min_peptide	The minimum number of peptides per protein to be considered a RESP candidate. Default is 4.
FDR	The FDR used to obtained the final p-value cutoff. Default is 0.01
comb_pv_method	The method used to combine p-values. Either george, fisher or edgington. Default is george. See Details.
RESP_score	The RESP score cutoff. Default is 0.5
fixed_score_cutoff	Logical to tell if you want to use a fixed cutoff for the RESP score. Default is FALSE. See Details.
categorize	Logical to categorize or not the obtained hits using the function imprints_categorize_peptides. Default is TRUE.
curvature	The curvature used for the curve on the volcano plot
folder_name	The name of the folder in which you want to save the results.

Details

The idea of this function is to compute the sum from all fold change for each peptide and then compute the cumulative sum of these summed fold change of every peptides for each protein. If the protein is not cleaved, this cumulative sum should be constantly increasing/decreasing, i.e linear. If the protein is cleaved, then this cumulative sum will either be convex or concave. If convex, the last peptides are more abundant; if concave the first peptides are more abundant. In the end a volcano plot will be plotted where the p-value corresponds to the combined p-value from the six temperatures comparison between peptides located towards the N-terminal and the ones located towards the C-terminal position. You can then use the function imprints_sequence_peptides to plot the peptides before and after the potential cleavage site.

George's method correspond to the sum of the logit of the p-values, Fisher's to the sum of the log of the p-values and Edgington's is the sum of the p-values. Edgington's method is the most stringent and is particularly sensitive with higher p-values whereas Fisher's method is the less stringent as it is mostly sensitive to low p-values. George's method is a compromise between the two methods. For more details read https://doi.org/10.48550/arXiv.1707.06897.

About the fixed_score_cutoff,if TRUE, the value RESP_score will directly be used as the cutoff and for all treatments. If FALSE, the RESP score cutoff will be calculated as the value selected for RESP_score plus the median of the scores of the proteins which have a p-value lower than the median of all p-values for a given treatment.

Value

The potential cleaved sites from the proteins considered as cleaved. A folder will also be saved where you'll find a volcano plots and results data.

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