artmsQualityControlEvidenceBasic: Quality Control analysis of the MaxQuant evidence file

In biodavidjm/artMS: Analytical R tools for Mass Spectrometry

Quality Control analysis of the MaxQuant evidence file

Description

Quality Control analysis of the MaxQuant evidence file

Usage

artmsQualityControlEvidenceBasic(
  evidence_file,
  keys_file,
  prot_exp = c("AB", "PH", "UB", "AC", "APMS", "PTM:XXX:yy"),
  output_dir = "qc_basic",
  output_name = "qcBasic_evidence",
  isSILAC = FALSE,
  plotINTDIST = FALSE,
  plotREPRO = FALSE,
  plotCORMAT = TRUE,
  plotINTMISC = TRUE,
  plotPTMSTATS = TRUE,
  printPDF = TRUE,
  verbose = TRUE
)

Arguments

evidence_file	(char or data.frame) The evidence file path and name, or data.frame
keys_file	(char or data.frame) The keys file path and name or data.frame
prot_exp	(char) Proteomics experiment. 6 options available: APMS: affinity purification mass spectrometry AB: protein abundance PH: protein phosphorylation UB: protein ubiquitination (aka ubiquitylation) AC: protein acetylation PTM:XXX:yy : User defined PTM. Replace XXX with 1 or more 1-letter amino acid codes on which to find modifications (all uppercase). Replace yy with modification name used within the evidence file (require lowercase characters). Example for phosphorylation: PTM:STY:ph will find modifications on aa S,T,Y with this example format ⁠_AAGGAPS(ph)PPPPVR_⁠. This means that the user could select phosphorylation as PH or PTM:STY:ph
output_dir	(char) Name for the folder to output the results plots. Default is "qc_basic".
output_name	(char) prefix output name (no extension). Default: "qcBasic_evidence"
isSILAC	if TRUE processes SILAC input files. Default is FALSE
plotINTDIST	if TRUE plots both Box-dot plot and Jitter plot of biological replicates based on MS (raw) intensity values, otherwise FALSE (default)
plotREPRO	if TRUE plots a correlation dotplot for all the combinations of biological replicates of conditions, based on MS Intensity values using features (peptide+charge). Otherwise FALSE (default)
plotCORMAT	if TRUE (default) plots a Correlation matrix for all the biological replicates using MS Intensity values, Clustering matrix of the MS Intensities
plotINTMISC	if TRUE (default) plots several pages, including bar plots of Total Sum of Intensities in BioReplicates, Total Sum of Intensities in Conditions, Total Peptide Counts in BioReplicates, Total Peptide Counts in conditions separated by categories: CON: contaminants, PROT peptides, REV reversed sequences used by MaxQuant to estimate the FDR; Box plots of MS Intensity values per biological replicates and conditions; bar plots of total intensity (excluding contaminants) by bioreplicates and conditions; Barplots of total feature counts by bioreplicates and conditions.
plotPTMSTATS	IF TRUE (default) plots stats related to the selected modification, including: bar plot of peptide counts and intensities, broken by PTM/other categories; bar plots of total sum-up of MS intensity values by other/PTM categories.
printPDF	If TRUE (default) prints out the pdfs. Warning: plot objects are not returned due to the large number of them.
verbose	(logical) TRUE (default) shows function messages

Value

Quality control files and plots

Examples

artmsQualityControlEvidenceBasic(evidence_file = artms_data_ph_evidence,
                                 keys_file = artms_data_ph_keys, 
                                 prot_exp =  "PH", 
                                 isSILAC = FALSE,
                                 plotINTDIST = FALSE,
                                 plotREPRO = TRUE,
                                 plotCORMAT = FALSE,
                                 plotINTMISC = FALSE,
                                 plotPTMSTATS = FALSE,
                                 printPDF = FALSE,
                                 verbose = FALSE)

# But we recommend the following test:
# 1. Go to a working directory: 
# setwd("/path/to/your/working/directory/")
# 2. Run the following command to print out all the pdf files
# artmsQualityControlEvidenceBasic(evidence_file = artms_data_ph_evidence,
#                                  keys_file = artms_data_ph_keys, 
#                                  prot_exp =  "PH")
# 3. Check your working directory and you should find pdf files with 
# all the QC plots

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