artmsAvgIntensityRT {artMS} | R Documentation

## Summarize average intensity and retention time per protein

### Description

Input an evidence file from MaxQuant and a file containing a list of proteins of interest (optional). The function will summarize from the evidence file and report back the average intensity, average retention time, and the average caliberated retention time. If a list of proteins is provided, then only those proteins will be summarized and returned.

### Usage

    artmsAvgIntensityRT(
      evidence_file,
      protein_file = NULL,
      output_file = FALSE,
      species,
      verbose = TRUE
    )

### Arguments

`evidence_file` | (char) The filepath to the MaxQuant searched data (evidence) file (txt tab delimited file).
`protein_file` | (char) The filepath to a file or vector conatining a list of proteins of interest.
`output_file` | (char) The file name for the results (must have the extension `.txt`). If empty, then the results will be returned as an R object.
`species` | (char) The species name. Check `?artmsMapUniprot2Entrez` for supported species
`verbose` | (logical) `TRUE` (default) shows function messages

### Value

An R object with the results and a file with the results (if the output_file argument is provided). It contains averages of Intensity, Retention Time, Caliberated Retention Time

### Examples

    ave_int <- artmsAvgIntensityRT(evidence_file = artms_data_ph_evidence,
                                      species = "human")

[Package artMS version 1.6.5 Index]