R/qualityControlEvidenceBasic.R
artmsQualityControlEvidenceBasic.Rd
Quality Control analysis of the MaxQuant evidence file
artmsQualityControlEvidenceBasic( evidence_file, keys_file, prot_exp = c("AB", "PH", "UB", "AC", "APMS"), fractions = 0, output_name = "qcBasic_evidence", isSILAC = FALSE, plotINTDIST = FALSE, plotREPRO = FALSE, plotCORMAT = TRUE, plotINTMISC = TRUE, plotPTMSTATS = TRUE, printPDF = TRUE, verbose = TRUE )
evidence_file | (char or data.frame) The evidence file path and name, or data.frame |
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keys_file | (char or data.frame) The keys file path and name or data.frame |
prot_exp | (char) Proteomics experiment. 4 options available:
|
fractions | (binary) Is a fractionated experiment?
|
output_name | (char) prefix output name (no extension). Default: "qcBasic_evidence" |
isSILAC | if |
plotINTDIST | if |
plotREPRO | if |
plotCORMAT | if
|
plotINTMISC | if |
plotPTMSTATS | IF |
printPDF | If |
verbose | (logical) |
Quality control files and plots
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