MSstatsPrepareForDataProcess: Prepare data for processing by 'dataProcess' function

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

Prepare data for processing by 'dataProcess' function

Description

Prepare data for processing by 'dataProcess' function

Usage

MSstatsPrepareForDataProcess(input, log_base, fix_missing)

Arguments

input	'data.table' in MSstats format
log_base	base of the logarithm to transform intensities
fix_missing	str, optional. Defaults to NULL, which means no action. If not NULL, must be one of the options: "zero_to_na" or "na_to_zero". If "zero_to_na", Intensity values equal exactly to 0 will be converted to NA. If "na_to_zero", missing values will be replaced by zeros.

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.