lfq_quant_analysis: Run Pairwise Protein Quantification on a level of LFQ...

In MassDynamics/lfq_processing: Processes Proteomics Files for Quantification.

Run Pairwise Protein Quantification on a level of LFQ Maxquant output

Description

Run Pairwise Protein Quantification on a level of LFQ Maxquant output

Usage

lfq_quant_analysis(
  dt,
  des,
  id_var,
  output_folder,
  quant_fn,
  dt_int_fn,
  conditions_dict = conditions_dict,
  imputeStDev = imputeStDev,
  imputePosition = imputePosition
)

Arguments

dt	A maxquant txt output text file (eg: proteinGroups.txt)
des	An experiment design file.
id_var	A column in dt identifying the unit (eg: majority.protein.id)
output_folder	An output folder to store produced files
quant_fn	A quantitative results file name
dt_int_fn	An intensity results file name
conditions_dict	A table with original and R-safe condition names
imputePosition	The Position parameter for MNAR Imputation
imputStDev	The Standard Deviation parameter for MNAR Imputation

Value

a list containing the quantitative results first and intentisty results second.

Examples

## Not run: 
#producing results per modified peptide id
mod_pep_list <- lfq_quant_analysis(mod_pept, expdes, id_var = "id", output_folder,
 "modificationSpecificPeptides_quant.txt",
 "modificationSpecificPeptides_quant_intensities.txt",
 conditions_dict=conditions_dict,
 imputeStDev = imputeStDev,
 imputePosition = imputePosition)

mod_pept <- mod_pep_list[[1]]
mod_pept_int <- mod_pep_list[[2]]

## End(Not run)

MassDynamics/lfq_processing documentation built on May 4, 2023, 11:20 p.m.