getProcessed: Get feature-level data to be used in the...

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

Get feature-level data to be used in the MSstatsSummarizationOutput function

Description

Get feature-level data to be used in the MSstatsSummarizationOutput function

Usage

getProcessed(input)

Arguments

input

data.table processed by dataProcess subfunctions

Value

data.table processed by dataProcess subfunctions

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_all = MSstatsSelectFeatures(input, "all") # all features
input_5 = MSstatsSelectFeatures(data.table::copy(input), 
"topN", top_n = 5) # top 5 features

proc1 = getProcessed(input_all)
proc2 = getProcessed(input_5)

proc1
proc2

MeenaChoi/MSstats documentation built on Nov. 10, 2024, 2:43 p.m.