artmsEvidenceToSAINTq: MaxQuant evidence file to SAINTq format

View source: R/evidenceToSAINTqFormat.R

artmsEvidenceToSAINTqR Documentation

MaxQuant evidence file to SAINTq format

Description

Converts the MaxQuant evidence file to the required files by SAINTq. The user can choose to use either peptides with ⁠spectral counts⁠ (use msspc) or the all the peptides (use all) for the analysis. The quantitative can be also chosen (either MS Intensity or Spectral Counts)

Usage

artmsEvidenceToSAINTq(
  evidence_file,
  keys_file,
  output_dir = "artms_saintq",
  sc_option = c("all", "msspc"),
  fractions = FALSE,
  quant_variable = c("msint", "msspc"),
  verbose = TRUE
)

Arguments

evidence_file

(char or data.frame) The evidence file path and name, or data.frame

keys_file

(char) Keys file with a SAINT column specifying test (T) and control (C) conditions

output_dir

(char) New directory to create and save files. Default is current directory (recommended to provide a new folder name).

sc_option

(char). Filter peptides with spectral counts only. Two options:

  • msspc: use only peptides with spectral_counts

  • all (default): all peptides detected (including the one resulting from the MaxQuant 'Match between run' algorithm)

fractions

(logical) TRUE for 2D proteomics (fractions). Default: FALSE

quant_variable

(char) Select the quantitative variable. Two options available:

  • msint: MS Intensity (default)

  • msspc: MS.MS.count (Spectral Counts)

verbose

(logical) TRUE (default) shows function messages

Details

After running the script, the new specified folder should contain the folling files:

  • saintq-config-peptides

  • saintq-config-proteins

  • saintq_input_peptides.txt

  • saintq_input_proteins.txt

Then cd into the new folder and run either of the following two options (assuming that saintq is installed in your linux/unix/mac os x system):

⁠> saintq config-saintq-peptides⁠

or

⁠> saintq config-saintq-proteins⁠

Value

The input files requires to run SAINTq

Examples

# Testing that the files cannot be empty
artmsEvidenceToSAINTq   (evidence_file = NULL, 
                                   keys_file = NULL, 
                                   output_dir = NULL)

biodavidjm/artMS documentation built on July 7, 2023, 12:24 p.m.