calculateProteolyticResistance: Calcutates proteolytic resistance for provided data. Requires...

In Vitek-Lab/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Calcutates proteolytic resistance for provided data. Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data.

Description

Calcutates proteolytic resistance for provided data. Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data.

Usage

calculateProteolyticResistance(
  LiP_data,
  fasta_file,
  differential_analysis = FALSE,
  contrast.matrix = "pairwise"
)

Arguments

LiP_data	name of variable containing LiP data. Must be output of dataSummarizationLiP function.
fasta_file	name of variable containing FASTA data. If FASTA file has not been processed please run the tidyFasta() function on it before inputting into this function. Protein names in file must match those in LiP_data.
differential_analysis	logical indicating whether to run differential analysis. Default is FALSE. Conditions and run numbers must match between the LiP and TrP data.
contrast.matrix	either a string of "pairwise" or a matrix including what comparisons to make in the differential analysis. Only required if differential_analysis=TRUE. Default is "pairwise".

Value

a data.frame including either the summarized Proteolytic data or differential analysis depending on parameter selection.

Examples

fasta <- tidyFasta(system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP"))
#calculateProteolyticResistance(MSstatsLiP_data, fasta)

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.