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tonywu1999 merged 3 commits into from
Feb 10, 2026
Merged

deprecation(groupComparisonPTM): Deprecate data.type parameter #124

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deprecation(groupComparisonPTM): Deprecate data.type parameter
tonywu1999 Feb 8, 2026
eb1c25f
match arguments
tonywu1999 Feb 10, 2026
1c251c1
remove logs
tonywu1999 Feb 10, 2026
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65 changes: 13 additions & 52 deletions R/groupComparisonPTM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,16 @@
#' function \code{\link[MSstatsPTM]{dataSummarizationPTM}} or
#' \code{\link[MSstatsPTM]{dataSummarizationPTM_TMT}} depending on acquisition
#' type.
#' @param data.type Type of data. Must be one of `LF` or `TMT`. Will be deprecated
#' in favor of ptm_label_type and protein_label_type.
#' @param contrast.matrix comparison between conditions of interests. Default
#' models full pairwise comparison between all conditions
#' @param ptm_label_type Type of quantification used in the PTM dataset.
#' Must be either `"LF"` (label-free) or `"TMT"` (Tandem Mass Tag isobaric labeling).
#' Choose `"LF"` for label-free quantification or `"TMT"` for TMT-labeled experiments.
#' Default is `"LF"`.
#' @param protein_label_type Type of quantification used in the protein dataset.
#' Must be either `"LF"` (label-free) or `"TMT"` (Tandem Mass Tag isobaric labeling).
#' Choose `"LF"` for label-free quantification or `"TMT"` for TMT-labeled experiments.
#' Default is `"LF"`.
#' @param moderated For TMT experiments only. TRUE will moderate t statistic;
#' FALSE (default) uses ordinary t statistic. Default is FALSE.
#' @param adj.method For TMT experiments only. Adjusted method for multiple
Expand All @@ -42,10 +48,6 @@
#' If not provided, such a file will be created automatically.
#' If `append = TRUE`, has to be a valid path to a file.
#' @param base start of the file name.
#' @param ptm_label_type Indicator of labeling type for PTM dataset. Must be one
#' of `LF` or `TMT`
#' @param protein_label_type Indicator of labeling type for PROTEIN dataset.
#' Must be one of `LF` or `TMT`
#' @return list of modeling results. Includes PTM, PROTEIN, and ADJUSTED
#' data.tables with their corresponding model results.
#'
Expand All @@ -56,8 +58,9 @@
#' protein_label_type="LF",
#' verbose = FALSE)
groupComparisonPTM = function(data,
data.type = NULL,
contrast.matrix = "pairwise",
ptm_label_type = c("LF", "TMT"),
protein_label_type = c("LF", "TMT"),
moderated = FALSE,
adj.method = "BH",
log_base = 2,
Expand All @@ -66,37 +69,11 @@ groupComparisonPTM = function(data,
append = FALSE,
verbose = TRUE,
log_file_path = NULL,
base = "MSstatsPTM_log_",
ptm_label_type = "LF",
protein_label_type = "LF") {

## Start log
# if (is.null(log_file_path) & use_log_file == TRUE){
# time_now = Sys.time()
# path = paste0(base, gsub("[ :\\-]", "_", time_now),
# ".log")
# file.create(path)
# } else {path = log_file_path}
#
# if (data.type == 'TMT'){
# pkg = "MSstatsTMT"
# option_log = "MSstatsTMTLog"
# } else {
# pkg = "MSstats"
# option_log = "MSstatsLog"
# }
#
# MSstatsLogsSettings(use_log_file, append,
# verbose, log_file_path = path,
# pkg_name = pkg)

# getOption(option_log)("INFO", "Starting parameter and data checks..")
if (!is.null(data.type) && (data.type == "TMT" || data.type == "LF")) {
ptm_label_type = data.type
protein_label_type = data.type
}
base = "MSstatsPTM_log_") {

Label = Site = NULL
ptm_label_type = match.arg(ptm_label_type)
protein_label_type = match.arg(protein_label_type)

data.ptm = data[["PTM"]]
data.protein = data[["PROTEIN"]]
Expand All @@ -111,7 +88,6 @@ groupComparisonPTM = function(data,

## Create pairwise matrix for label free
if (contrast.matrix[1] == "pairwise"){
# getOption(option_log)("INFO", "Building pairwise matrix.")
if ("GROUP" %in% colnames(data.ptm$ProteinLevelData)) {
labels <- unique(data.ptm$ProteinLevelData$GROUP)
} else if ("Condition" %in% colnames(data.ptm$ProteinLevelData)) {
Expand All @@ -125,7 +101,6 @@ groupComparisonPTM = function(data,
## PTM Modeling
message("Starting PTM modeling...")
if (ptm_label_type == "TMT"){
# getOption(option_log)("INFO", "Starting TMT PTM Model")
ptm_model_full = groupComparisonTMT(data.ptm,
contrast.matrix = contrast.matrix,
moderated = moderated,
Expand All @@ -139,7 +114,6 @@ groupComparisonPTM = function(data,
ptm_model_site_sep = ptm_model_full$ComparisonResult
ptm_model_details = ptm_model_full$FittedModel
} else if (ptm_label_type == "LF") {
# getOption(option_log)("INFO", "Starting non-TMT PTM Model")
ptm_model_full = groupComparison(contrast.matrix,
data.ptm, save_fitted_models, log_base)#,
# use_log_file, append, verbose,
Expand All @@ -156,7 +130,6 @@ groupComparisonPTM = function(data,
## Protein Modeling
message("Starting Protein modeling...")
if (protein_label_type == "TMT"){
# getOption(option_log)("INFO", "Starting TMT Protein Model")
protein_model_full = groupComparisonTMT(data.protein,
contrast.matrix = contrast.matrix,
moderated = moderated,
Expand All @@ -169,7 +142,6 @@ groupComparisonPTM = function(data,
protein_model = protein_model_full$ComparisonResult
protein_model_details = protein_model_full$FittedModel
} else if (protein_label_type == "LF") {
# getOption(option_log)("INFO", "Starting non-TMT Protein Model")
protein_model_full = groupComparison(contrast.matrix,
data.protein, save_fitted_models,
log_base, use_log_file)#,
Expand All @@ -183,20 +155,16 @@ groupComparisonPTM = function(data,
protein_model = as.data.table(protein_model)

message("Starting adjustment...")
# getOption(option_log)("INFO", "Starting Protein Adjustment")
ptm_model_site_sep = copy(ptm_model)

## extract global protein name
ptm_model_site_sep = .extractProtein(ptm_model_site_sep, protein_model)
# getOption(option_log)("INFO", "Rcpp function extracted protein info")

## adjustProteinLevel function can only compare one label at a time
comparisons = unique(ptm_model_site_sep[, Label])

adjusted_model_list = list()
for (i in seq_len(length(comparisons))) {
# getOption(option_log)("INFO", paste0("Adjusting for Comparison - ",
# as.character(i)))
temp_adjusted_model = .applyPtmAdjustment(comparisons[[i]],
ptm_model_site_sep,
protein_model)
Expand Down Expand Up @@ -235,19 +203,12 @@ groupComparisonPTM = function(data,
use.names=TRUE)
adjusted_models = adjusted_models[!is.na(adjusted_models$Protein)]

# getOption(option_log)("INFO", "Adjustment complete, returning models.")
models = list('PTM.Model'=ptm_model,
'PROTEIN.Model'=protein_model,
'ADJUSTED.Model'=adjusted_models,
'Model.Details'=list('PTM'=ptm_model_details,
'PROTEIN'=protein_model_details))
}

if (!is.null(data.type) && (data.type == "TMT" || data.type == "LF")) {
warning("DEPRECATION NOTICE: The `data.type` argument is being deprecated.
Please use `ptm_label_type` and `protein_label_type` instead ahead
of Release 3.22")
}

return(models)

Expand Down
26 changes: 13 additions & 13 deletions man/groupComparisonPTM.Rd
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