Man pages for computational-metabolomics/qcrms
Creates quality control output from XCMS output
| createClassAndColors | Function to create sorted class labels and colors for... |
| createProjectHeader | Create a header for QC report |
| createQCreport | Create a pdf output from data slots on QCreportObject |
| createQCreportObject | Create initial qcrepotobject structure from input variable |
| createXlsx | Create xlsx output file from XCMS output |
| doPCA | Perform PCA analysis ot single data set or list of data sets |
| doSummaryPlot | Wrapper function to generate PCA plot and RSD statistics plot |
| do_variability_list | Calculate RSD% or MAD values per sample group of input... |
| do_variability_plot | Plot violin plots from the dolist_object fucntion output |
| do_variability_table | Create summary table of list object containing variabilty... |
| EICs | Create plots for EICs |
| file_type | Check if input is a text file or xlsx file |
| get_file_extension | Return file extension from character vector if file paths |
| getPeaklistW4M | This function prepares peaklist object from xcms output |
| locate_raw_files | Locate raw LC/MS raw files on local files system and align... |
| meta_data_from_filenames | Generate meta data from sample filenames |
| missingValues | Create QCreport data object to asses missing values |
| mzML.startTimeStamp | Extract measurement time stamp fro mzML data file |
| PCA | Perform severl PCA models and create plots |
| prepare_boxplot_multiple_batches | Prepare data for ggplot barplot |
| prepareData | Wrapper function to transform data for statistical analysis |
| QC | Create QC quality plots |
| RSDstatistics | Create QCreport data object to asses RSD |
| RTstabilityAssement | Several diagnostic tables and plot for retention time and m/z... |
| sampleSummary | Exctract and return ggplot2 object of EICs for specified xmcm... |
| sampleSummaryPlots | Create plots of TIC chromatograms and general sample summary. |
| SignalBatchCorrection | Apply signal batch correction |
| testData | Testing data set |
| theme_Publication | Ggplot publication theme |
| XCMS_EIC_plot | Exctract and return ggplot2 object of EICs for specified xcms... |
