Man pages for computational-metabolomics/qcrms
Creates quality control output from XCMS output

createClassAndColorsFunction to create sorted class labels and colors for...
createProjectHeaderCreate a header for QC report
createQCreportCreate a pdf output from data slots on QCreportObject
createQCreportObjectCreate initial qcrepotobject structure from input variable
createXlsxCreate xlsx output file from XCMS output
doPCAPerform PCA analysis ot single data set or list of data sets
doSummaryPlotWrapper function to generate PCA plot and RSD statistics plot
do_variability_listCalculate RSD% or MAD values per sample group of input...
do_variability_plotPlot violin plots from the dolist_object fucntion output
do_variability_tableCreate summary table of list object containing variabilty...
EICsCreate plots for EICs
file_typeCheck if input is a text file or xlsx file
get_file_extensionReturn file extension from character vector if file paths
getPeaklistW4MThis function prepares peaklist object from xcms output
locate_raw_filesLocate raw LC/MS raw files on local files system and align...
meta_data_from_filenamesGenerate meta data from sample filenames
missingValuesCreate QCreport data object to asses missing values
mzML.startTimeStampExtract measurement time stamp fro mzML data file
PCAPerform severl PCA models and create plots
prepare_boxplot_multiple_batchesPrepare data for ggplot barplot
prepareDataWrapper function to transform data for statistical analysis
QCCreate QC quality plots
RSDstatisticsCreate QCreport data object to asses RSD
RTstabilityAssementSeveral diagnostic tables and plot for retention time and m/z...
sampleSummaryExctract and return ggplot2 object of EICs for specified xmcm...
sampleSummaryPlotsCreate plots of TIC chromatograms and general sample summary.
SignalBatchCorrectionApply signal batch correction
testDataTesting data set
theme_PublicationGgplot publication theme
XCMS_EIC_plotExctract and return ggplot2 object of EICs for specified xcms...
computational-metabolomics/qcrms documentation built on Jan. 18, 2021, 1:46 a.m.