MSstatsPrepareForSummarization: Prepare feature-level data for protein-level summarization

In Vitek-Lab/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Prepare feature-level data for protein-level summarization

Description

Prepare feature-level data for protein-level summarization

Usage

MSstatsPrepareForSummarization(
  input,
  method,
  impute,
  censored_symbol,
  remove_uninformative_feature_outlier
)

Arguments

input	feature-level data processed by dataProcess subfunctions
method	summarization method - 'summaryMethod' parameter of the dataProcess function
impute	if TRUE, censored missing values will be imputed - 'MBimpute' parameter of the dataProcess function
censored_symbol	censored missing value indicator - 'censoredInt' parameter of the dataProcess function
remove_uninformative_feature_outlier	if TRUE, features labeled as outlier of uninformative by the MSstatsSelectFeatures function will not be used in summarization

Value

data.table

Examples

raw = DDARawData 
method = "TMP"
cens = "NA"
impute = TRUE
MSstatsConvert::MSstatsLogsSettings(FALSE)
input = MSstatsPrepareForDataProcess(raw, 2, NULL)
head(input)

Vitek-Lab/MSstats documentation built on April 21, 2024, 10:14 p.m.