dot-summarizeMSstats: Summarization based on MSstats

In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Summarization based on MSstats

Description

Summarization based on MSstats

Usage

.summarizeMSstats(
  input,
  annotation,
  impute,
  max_quantile_censored = NULL,
  log_file_path = NULL
)

Arguments

input	data.table
annotation	data.table with run and channel annotation
impute	only for method="msstats". TRUE (default) imputes missing values by Accelated failure model. FALSE uses minimum value to impute the missing value for each peptide precursor ion.
max_quantile_censored	We assume missing values are censored. maxQuantileforCensored is Maximum quantile for deciding censored missing value, for instance, 0.999. Default is Null.
log_file_path	path to a MSstats log file

Value

data.table

Vitek-Lab/MSstatsTMT documentation built on Nov. 18, 2024, 11:30 a.m.