MSstatsHandleMissing: Handle censored missing values

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

Handle censored missing values

Description

Handle censored missing values

Usage

MSstatsHandleMissing(
  input,
  summary_method,
  impute,
  missing_symbol,
  censored_cutoff
)

Arguments

input	'data.table' in MSstats data format
summary_method	summarization method ('summaryMethod' parameter to 'dataProcess')
impute	if TRUE, missing values are supposed to be imputed ('MBimpute' parameter to 'dataProcess')
missing_symbol	'censoredInt' parameter to 'dataProcess'
censored_cutoff	'maxQuantileforCensored' parameter to 'dataProcess'

Value

data.table

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)
head(input)
 

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