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

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

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,
  data.type,
  contrast.matrix = "pairwise",
  moderated = FALSE,
  adj.method = "BH",
  log_base = 2,
  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.
data.type	string indicating experimental acquisition type. "TMT" is used for TMT labeled experiments. For all other experiments (Label Free/ DDA/ DIA) use "LabelFree".
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 experiemnts 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.
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, 
                                     data.type = "LabelFree",
                                     verbose = FALSE)

Vitek-Lab/MSstatsPTM documentation built on Feb. 7, 2025, 7:44 p.m.