limmaStatsFun: This function performs the differential expression analysis...

In MassDynamics/MassExpression: MassExpression

This function performs the differential expression analysis with limma including all pairwise comparisons using the condition provided

Description

This function performs the differential expression analysis with limma including all pairwise comparisons using the condition provided

Usage

limmaStatsFun(
  ID_type,
  int_type,
  condition_col_name,
  run_id_col_name,
  rep_col_name,
  funDT,
  returnDecideTestColumn,
  conditionSeparator,
  pairwise.comp = NULL,
  all.comparisons = TRUE
)

Arguments

ID_type	str. Column name of feature ID, e.g. 'ProteinId'
int_type	str. Column name containing intensities to use for the differential expression analysis, e.g. 'log2NIntNorm'
condition_col_name	str. Column name for the condition of interest, e.g. 'Condition'. Used to build all pairwise comparisons.
run_id_col_name	str. Column name for the unique identifier of condition and replicate, e.g. 'RunId'
rep_col_name	str. Replicate column name. e.g. 'Replicate'
funDT	data.table. long table containing intensities for all proteins and samples.
returnDecideTestColumn	logical. If TRUE the row data of the 'CompleteIntensityExperiment' will contain the output from 'limma::decideTests'.
conditionSeparator	string. String used to separate up and down condition in output.
pairwise.comp	chr. XX In the future this will allow the possibility of including only some pairwise comparisons of interest.
all.comparisons	logical. TRUE to run differential expression analysis for all pairwise comparisons.

MassDynamics/MassExpression documentation built on May 7, 2023, 11:29 a.m.