artmsAnalysisQuantifications {artMS} | R Documentation |
Analysis of relative quantifications, including:
Annotations
Summary files in different format (xls, txt) and shapes (long, wide)
Numerous summary plots
Enrichment analysis using Gprofiler
PCA of quantifications
Clustering analysis
Basic imputation of missing values
artmsAnalysisQuantifications(log2fc_file, modelqc_file, species, output_dir = ".", enrich = TRUE, l2fc_thres = 1.5, choosePvalue = c("adjpvalue", "pvalue"), isBackground = "nobackground", isPtm = "global", mnbr = 2, isFluomics = FALSE, pathogen = "nopathogen", plotPvaluesLog2fcDist = TRUE, plotAbundanceStats = TRUE, plotReproAbundance = TRUE, plotCorrConditions = TRUE, plotCorrQuant = TRUE, plotPCAabundance = TRUE, plotFinalDistributions = TRUE, plotPropImputation = TRUE, plotHeatmapsChanges = TRUE, plotTotalQuant = TRUE, plotClusteringAnalysis = TRUE, verbose = TRUE)
log2fc_file |
(char) MSstats results file location |
modelqc_file |
(char) MSstats modelqc file location |
species |
(char) Select one species. Species currently supported for a full analysis (including enrichment analysis):
To find out species supported only for annotation check
|
output_dir |
(char) Name for the folder to output the results from the function. Default is current directory (recommended to provide a new folder name). |
enrich |
(logical) Performed enrichment analysis using GprofileR?
Only available for species HUMAN and MOUSE.
|
l2fc_thres |
(int) log2fc cutoff for enrichment analysis (default,
|
choosePvalue |
(char) specify whether |
isBackground |
(char) background of gene names for enrichment analysis.
|
isPtm |
(char) Is a ptm-site quantification?
|
mnbr |
(int) minimal number of biological replicates for imputation
and filtering. Default: |
isFluomics |
(logical) Does this data belong to the FluOMICs project?
|
pathogen |
(char) Is there a pathogen in the dataset as well?
if it does not, then use |
plotPvaluesLog2fcDist |
(logical) If |
plotAbundanceStats |
(logical) If |
plotReproAbundance |
(logical) If |
plotCorrConditions |
(logical) If |
plotCorrQuant |
(logical) if |
plotPCAabundance |
(logical) if |
plotFinalDistributions |
(logical) if |
plotPropImputation |
(logical) if |
plotHeatmapsChanges |
(logical) if |
plotTotalQuant |
(logical) if |
plotClusteringAnalysis |
(logical) if |
verbose |
(logical) |
(data.frame) summary of quantifications, including annotations, enrichments, etc
# Testing that the files cannot be empty artmsAnalysisQuantifications(log2fc_file = NULL, modelqc_file = NULL, species = NULL, output_dir = NULL)