groupComparisonLiP: Model LiP and TrP data and make adjustments if needed Returns...

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

Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasets

Description

Takes summarized LiP peptide and TrP protein data from dataSummarizationLiP If global protein data is unavailable, LiP data only can be passed into the function. Including protein data allows for adjusting LiP Fold Change by the change in global protein abundance..

Usage

groupComparisonLiP(
  data,
  contrast.matrix = "pairwise",
  fasta.path = NULL,
  log_base = 2,
  use_log_file = FALSE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  base = "MSstatsLiP_log_"
)

Arguments

data	list of summarized datasets. Can be output of MSstatsLiP summarization function dataSummarizationLiP. Must include dataset named "LiP" as minimum.
contrast.matrix	comparison between conditions of interests. Default models full pairwise comparison between all conditions
fasta.path	a file path to a fasta file that includes the proteins listed in the data. Default is NULL. Include this parameter to determine trypticity of peptides in LiP models.
log_base	base of the logarithm used in dataProcess.
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be added to an existing log file.
verbose	logical. If TRUE, information about data processing will be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If append = TRUE, has to be a valid path to a file.
base	start of the file name.

Value

list of modeling results. Includes LiP, PROTEIN, and ADJUSTED LiP data.tables with their corresponding model results.

Examples

## Use output of dataSummarizationLiP function
fasta <- system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP")

# Test for pairwise comparison
MSstatsLiP_model <- groupComparisonLiP(MSstatsLiP_Summarized,
                                   contrast.matrix = "pairwise",
                                   fasta.path = fasta)

# Returns list of three models
names(MSstatsLiP_model)
head(MSstatsLiP_model$LiP.Model)
head(MSstatsLiP_model$TrP.Model)
head(MSstatsLiP_model$Adjusted.LiP.Model)

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