Quality Control analysis of the evidence-like metabolomics dataset

Source: R/qualityControlMetabolomics.R

Quality Control analysis of the evidence-like metabolomics dataset

artmsQualityControlMetabolomics(
  evidence_file,
  keys_file,
  met_exp = c("MV"),
  output_name = "qcPlots_metab",
  plotINTDIST = FALSE,
  plotCORMAT = TRUE,
  plotINTMISC = 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
met_exp

(char) Metabolomics experiment. Only one option available (so far):

  • MV: Markview output
output_name

(char) prefix output name (no extension). Default: "qcPlots_metab"
plotINTDIST

if TRUE (default) plots both Box-dot plot and Jitter plot of biological replicates based on MS (raw) intensity values.
plotCORMAT

if TRUE (default) generates up to 3 pdf files for technical replicates, biological replicates, and conditions. Each pdf file contains:

  • Correlation matrix for all the biological replicates using MS Intensity values,

  • Clustering matrix of the MS Intensities and correlation distribution

  • histogram of the distribution of correlations
plotINTMISC

if TRUE (default) plots several pages, including bar plots of Total Sum of Intensities in BioReplicates, Total Sum of Intensities in Conditions, Total Feature Counts in BioReplicates, Total Feature Counts in conditions separated by categories (INT: has a intensity value NOINT: no intensity value ) Box plots of MS Intensity values per biological replicates and conditions; bar plots of total intensity by bioreplicates and conditions; Barplots of total feature counts by bioreplicates and conditions.
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 for metabolomics

Examples

# Testing that input arguments cannot be null
artmsQualityControlMetabolomics(evidence_file = NULL,
                 keys_file = NULL,
                 met_exp = "MV")

#> [1] "Both <evidence_file> and <keys_file> cannot be NULL"