MSstatsSummarizeWithMultipleCores: Feature-level data summarization with multiple cores

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

Feature-level data summarization with multiple cores

Description

Feature-level data summarization with multiple cores

Usage

MSstatsSummarizeWithMultipleCores(
  input,
  method,
  impute,
  censored_symbol,
  remove50missing,
  equal_variance,
  numberOfCores = 1
)

Arguments

input	feature-level data processed by dataProcess subfunctions
method	summarization method: "linear" or "TMP"
impute	only for summaryMethod = "TMP" and censoredInt = 'NA' or '0'. TRUE (default) imputes 'NA' or '0' (depending on censoredInt option) by Accelated failure model. FALSE uses the values assigned by cutoffCensored
censored_symbol	Missing values are censored or at random. 'NA' (default) assumes that all 'NA's in 'Intensity' column are censored. '0' uses zero intensities as censored intensity. In this case, NA intensities are missing at random. The output from Skyline should use '0'. Null assumes that all NA intensites are randomly missing.
remove50missing	only for summaryMethod = "TMP". TRUE removes the runs which have more than 50% missing values. FALSE is default.
equal_variance	only for summaryMethod = "linear". Default is TRUE. Logical variable for whether the model should account for heterogeneous variation among intensities from different features. Default is TRUE, which assume equal variance among intensities from features. FALSE means that we cannot assume equal variance among intensities from features, then we will account for heterogeneous variation from different features.
numberOfCores	Number of cores for parallel processing. When > 1, a logfile named 'MSstats_dataProcess_log_progress.log' is created to track progress. Only works for Linux & Mac OS. Default is 1.

Value

list of length one with run-level data.

Vitek-Lab/MSstats documentation built on May 2, 2024, 12:32 a.m.