lfq_transformer: Run Pairwise Protein Quantification on each level of LFQ...

In MassDynamics/lfq_processing: Processes Proteomics Files for Quantification.

Run Pairwise Protein Quantification on each level of LFQ Maxquant output

Description

Run Pairwise Protein Quantification on each level of LFQ Maxquant output

Usage

lfq_transformer(
  ma_tables,
  output_folder,
  imputeStDev = 0.3,
  imputePosition = 1.8,
  protein_only = FALSE
)

Arguments

output_folder	An output folder to store produced files.
imputePosition	The Position parameter for MNAR Imputation
protein_only	Boolean, TRUE means LFQ will only process protein level data
mq_folder	A maxquant txt output folder.
imputStDev	The Standard Deviation parameter for MNAR Imputation

Value

A string describing the type of experiment

Examples

## Not run: 
tmp =  lfq_transformer(mq_folder = upload_folder,
 output_folder = output_folder,
 imputeStDev=0.3,
 imputePosition=1.8)
# get each of the produced quantification files.
prot = tmp[[1]]
prot_int = tmp[[2]]
pept = tmp[[3]]
pept_int = tmp[[4]]
mod_pept = tmp[[5]]
mod_pept_int = tmp[[6]]
expdes = tmp[[7]]
evidence = tmp[[8]]
msms = tmp[[9]]

## End(Not run)

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