MSstatsNormalize: Normalize MS data

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

Normalize MS data

Description

Normalize MS data

Usage

MSstatsNormalize(
  input,
  normalization_method,
  peptides_dict = NULL,
  standards = NULL
)

Arguments

input	data.table in MSstats format
normalization_method	name of a chosen normalization method: "NONE" or "FALSE" for no normalization, "EQUALIZEMEDIANS" for median normalization, "QUANTILE" normalization for quantile normalization from 'preprocessCore' package, "GLOBALSTANDARDS" for normalization based on selected peptides or proteins.
peptides_dict	'data.table' of names of peptides and their corresponding features.
standards	character vector with names of standards, required if "GLOBALSTANDARDS" method was selected.

Value

data.table

Examples

raw = DDARawData 
method = "TMP"
cens = "NA"
impute = TRUE
MSstatsConvert::MSstatsLogsSettings(FALSE)
input = MSstatsPrepareForDataProcess(raw, 2, NULL)
input = MSstatsNormalize(input, "EQUALIZEMEDIANS") # median normalization
head(input)

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