imputationDIA: imputationDIA

In mgerault/DIAgui: A shiny app for processing DIAnn output in proteomics

imputationDIA

Description

Perform data imputation for your DIA data

Usage

imputationDIA(
  data,
  transformation = c("none", "log2"),
  iteration = 3,
  method = c("norm.predict", "zeros", "pmm", "midastouch", "sample", "cart", "rf",
    "mean", "norm", "norm.nob", "norm.boot", "lasso.norm", "lasso.select.norm", "knn",
    "MinDet", "MinProb", "QRILC")
)

Arguments

data	Processed data from DIAnn (from iq processing or diann_matrix for example)
transformation	Which transformation do you want to apply (log2 or none)
iteration	Number of iterations for the imputation. See mice and imputeLCMD for more details.
method	Method used for the imputation. See mice and imputeLCMD for more details.

Details

If your data contains iBAQ and or Top3 absolute quantification, then their column names should start with 'iBAQ_' and 'Top3_' respectively. Other numeric columns like the number of peptides used for quantification or the number of theoritical peptides will not be imputed, please keep the default name obtained with the app or the functions diann_matrix or diann_maxlfq.

Value

The imputed data

mgerault/DIAgui documentation built on Nov. 7, 2024, 12:12 a.m.