MSstatsSummarize: Feature-level data summarization

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

Feature-level data summarization

Description

Feature-level data summarization

Usage

MSstatsSummarize(
  proteins_list,
  method,
  impute,
  censored_symbol,
  remove50missing,
  equal_variance
)

Arguments

proteins_list	list of processed feature-level data
method	summarization method: "linear" or "TMP"
impute	only for summaryMethod = "TMP" and censoredInt = 'NA' or '0'. TRUE (default) imputes 'NA' or '0' (depending on censoredInt option) by Accelated failure model. FALSE uses the values assigned by cutoffCensored
censored_symbol	Missing values are censored or at random. 'NA' (default) assumes that all 'NA's in 'Intensity' column are censored. '0' uses zero intensities as censored intensity. In this case, NA intensities are missing at random. The output from Skyline should use '0'. Null assumes that all NA intensites are randomly missing.
remove50missing	only for summaryMethod = "TMP". TRUE removes the proteins where every run has at least 50% missing values for each peptide. FALSE is default.
equal_variance	only for summaryMethod = "linear". Default is TRUE. Logical variable for whether the model should account for heterogeneous variation among intensities from different features. Default is TRUE, which assume equal variance among intensities from features. FALSE means that we cannot assume equal variance among intensities from features, then we will account for heterogeneous variation from different features.

Value

list of length one with run-level data.

Examples

raw = DDARawData 
method = "TMP"
cens = "NA"
impute = TRUE
MSstatsConvert::MSstatsLogsSettings(FALSE)
input = MSstatsPrepareForDataProcess(raw, 2, NULL)
input = MSstatsNormalize(input, "EQUALIZEMEDIANS")
input = MSstatsMergeFractions(input)
input = MSstatsHandleMissing(input, "TMP", TRUE, "NA", 0.999)
input = MSstatsSelectFeatures(input, "all")
processed = getProcessed(input)
input = MSstatsPrepareForSummarization(input, method, impute, cens, FALSE)
input_split = split(input, input$PROTEIN)
summarized = MSstatsSummarize(input_split, method, impute, cens, FALSE, TRUE)
length(summarized) # list of summarization outputs for each protein
head(summarized[[1]][[1]]) # run-level summary

Vitek-Lab/MSstats documentation built on Nov. 4, 2024, 3:08 p.m.