MSstatsNormalize: Normalize MS data

View source: R/utils_normalize.R

MSstatsNormalizeR Documentation

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)


MeenaChoi/MSstats documentation built on July 13, 2024, 10:59 a.m.