artmsQualityControlMetabolomics {artMS} | R Documentation |
Quality Control analysis of the evidence-like metabolomics dataset
Description
Quality Control analysis of the evidence-like metabolomics
dataset
Usage
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):
|
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")
[Package
artMS version 1.11.2
Index]