MSstatsSummarizeSingleLinear: Linear model-based summarization for a single protein

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

Linear model-based summarization for a single protein

Description

Linear model-based summarization for a single protein

Usage

MSstatsSummarizeSingleLinear(single_protein, equal_variances = TRUE)

Arguments

single_protein	feature-level data for a single protein
equal_variances	if TRUE, observation are assumed to be homoskedastic

Value

list with protein-level data

Examples

raw = DDARawData 
method = "linear"
cens = NULL
impute = FALSE 
# currently, MSstats only supports MBimpute = FALSE for linear summarization
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")
input = MSstatsPrepareForSummarization(input, method, impute, cens, FALSE)
input_split = split(input, input$PROTEIN)
single_protein_summary = MSstatsSummarizeSingleLinear(input_split[[1]])
head(single_protein_summary[[1]])

MeenaChoi/MSstats documentation built on April 22, 2024, 9:36 p.m.