groupComparisonPTM: Perform differential analysis on MS-based proteomics...

View source: R/groupComparisonPTM.R

groupComparisonPTMR Documentation

Perform differential analysis on MS-based proteomics experiments targeting PTMs

Description

Takes summarized PTM and protein data from dataSummarizationPTM or dataSummarizationPTM_TMT functions and performs differential analysis. Leverages unmodified protein data to perform adjustment and deconvolute the effect of the PTM and unmodified protein. If protein data is unavailable, PTM data can still be passed into the function, however adjustment can not be performed. All model results are returned for completeness.

Usage

groupComparisonPTM(
  data,
  ptm_label_type,
  protein_label_type,
  contrast.matrix = "pairwise",
  moderated = FALSE,
  adj.method = "BH",
  log_base = 2,
  save_fitted_models = TRUE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  base = "MSstatsPTM_log_"
)

Arguments

data

list of summarized datasets. Output of MSstatsPTM summarization function dataSummarizationPTM or dataSummarizationPTM_TMT depending on acquisition type.

ptm_label_type

Indicator of labeling type for PTM dataset. Must be one of LF or TMT

protein_label_type

Indicator of labeling type for PROTEIN dataset. Must be one of LF or TMT

contrast.matrix

comparison between conditions of interests. Default models full pairwise comparison between all conditions

moderated

For TMT experiments only. TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic. Default is FALSE.

adj.method

For TMT experiments only. Adjusted method for multiple comparison. "BH" is default. "BH" is used for all other experiment types

log_base

For non-TMT experiments only. The base of the logarithm used in summarization.

save_fitted_models

logical, if TRUE, fitted models will be added to the output.

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 PTM, PROTEIN, and ADJUSTED data.tables with their corresponding model results.

Examples


model.lf.msstatsptm = groupComparisonPTM(summary.data, 
                                     ptm_label_type="LF",
                                     protein_label_type="LF",
                                     verbose = FALSE)

Vitek-Lab/MSstatsPTM documentation built on April 12, 2025, 11:54 p.m.