Package index • MSdev

All functions

get_MSdev_DEP_se() DEP_list_contrast() DEP_add_rejections() DEP_p_adjust() DEP_check_sig() DEP_test_diff() DEP_filter_significant() DEP_get_diff_table() DEP_plot_volcano() DEP.plot.volcano.lipidomic() DEP.plot.lfc.lipid.class() DEP_plot_heatmap() DEP_export_data() DEP_plot_PCA() DEP_pathway_enrich() DEP_pathway_enrich_gene() se_adjuset_by_weight() DEP_test_ANOVA() DEP_plot_single_bar() DEP_impute_mean() DEP_filter_miss() DEP_filter_QC_RSD() DEP_get_QC_RSD() DEP_preprocess() DEP_plot_normalization() get_DEP_se_group_color() get_DEP_se_sig_feature() get_DEP_se_from_ME_result() DEP_remove_QC(): DEP styled SummarizedExperiment and related analysis
export_MChromatograms_Metabolites(): Export MRM chromatograms as PDF
MS_Exp-class: MS_Exp-class
MSdev-feature-group-EIC: Feature-group EIC similarity, grouping, and reporting
MSdev(): Create an MSdev object
plotPathwayEnrichment(): Bioinformatic analysis
MSdev_save() MSdev_load(): MSdev input and output
MSdev_export(): Msdev Export
MSdev_get_feature_chrom(): Extract chromatograms for features
MSdev_get_feature_purity(): Compute MS1 feature purity for both polarities
MSdev_get_peak_table_from_spectra(): Build MS2 precursor peak table from spectra
MSdev_group_feature_EIC(): Group features by EIC similarity within RT tolerance
plot_MSdev_normalization() plot_MSdev_QC_RSD_hist() plot_MSdev_QC_RSD_CDF() plot_MSdev_TIC() plot_MSdev_PCA(): Plot Msdev Normalization
MSdev_processInfo(): List process history of xcmsData
MSdev_add_sample() MSdev_xcmsProcessing() MSdev_get_xcms() MSdev_set_param() plot_MSdev_sample_peaks() MSdev_checkSampleInfo() MSdev_import_sampleinfo() MSdev_msConvert() MSdev_extract_Spectra() MSdev_assign_MS2() MSdev_annotation() MSdev_annotation_MS2_Precursor() MSdev_get_Stat() MSdev_get_Se(): Add new sample files to MSdev object
MSdev_xcms_group_features(): Group features across samples using xcms
MetaboSignalNetworkTable2df(): MetaboSignalNetworkTable2df
MetaboSignalNetworkTableStandardNodeName(): MetaboSignalNetworkTableStandardNodeName
Report_MSdev_feature_group_EIC(): Report feature-group EIC mirror plots as PDFs
Spectra_filter_TIC(): Filter Spectra by TIC (Top N per group)
Spectra_filter_noise(): Filter Peaks Below Noise Level
Spectra_get_noise(): Estimate Noise Level for Spectra
Spectra_get_purity(): Estimate Precursor Purity for Mass Spectra
capture_base_plot(): capture_base_plot
colorMix(): Mix Colors with Alpha Blending
combineSpectra_ce_max_precursor(): Select Spectra with Maximum Precursor Intensity per Collision Energy
combineSpectra_groupby_ce(): Combine Spectra by Collision Energy
date_suffix(): Generate Date Suffix
df_to_wb(): df_to_wb
.xcms_has_features(): Whether an xcms object supports and currently has feature definitions. Plain MsExperiment has no hasFeatures method; only XcmsExperiment / XCMSnExp.
edit_df_in_excel(): edit_df_in_excel
export_MSdev_feature_MSMS(): Export MS/MS spectrum and chromatogram for a feature
export_Spectra_peak_list_for_cfm(): Export Spectra peak list for CFM (Deprecated)
export_graph2pdf(): Export Graph2pdf
extractSpectra_fullscan_DDA(): extractSpectra_fullscan_DDA
featureCandidate(): featureCandidate
featureSpectra_fullscan_DDA(): featureSpectra_fullscan_DDA
fella_igraph(): Generate FELLA Enrichment igraph
findISMSdev(): Find internal standard features in MSdev
fix_xcms_chromPeaks_mz_width(): Fix overly wide xcms chromPeaks mz window
get_CFM_data_Spectra(): Convert CFM Data to Spectra Object
get_MS_sampleinfo(): Generate sample information table from raw data files
get_MSdev_Chromatogram(): Retrieve feature chromatograms from MSdev object
get_MSdev_Spectra(): Retrieve spectra from MSdev object
get_MSdev_instrument(): MS instrument description from an MSdev object
get_MSdev_spectra_target_list(): Build MS2 spectra target list (mz/rt windows)
get_MSinfo_mzR(): Get Msinfo Mzr
get_Spectra_data(): Get Spectra Data
get_chroms_data(): get_chroms_data
get_features_from_xcms(): get_features_from_xcms
get_igraph_membership(): Connected-component membership for igraph vertices
get_matrix_value_fill_with_NA(): Subset a matrix with NA fill for missing rows/columns
get_node_info(): get_node_info
get_p_t_test(): Wrapper for t.test
get_xcms_Spectra(): get_xcms_Spectra
get_xcms_feature_EIC_similarity(): Pairwise EIC similarity for xcms features
get_xcms_feature_connect(): TODO: unfinished. Build isotope mass shift grid for multi-tracer
get_xcms_feature_purity_matrix(): Compute MS1 purity matrix for xcms features
get_xcms_roi_list(): Build xcms centWave roiList from mz/rt targets
getmsExpTime(): getmsExpTime
ggplot_roc(): ggplot_roc
ggplot_sum_patchwork(): ggplot_sum_patchwork
groupMz(): Group m/z Values by ppm Tolerance
groupSimilarityMatrix_completeLinkage(): Group features by complete-linkage similarity threshold
groupSimilarityMatrix_hclustAverage(): Group features by average-linkage hierarchical clustering on similarity
groupStringFactor(): groupStringFactor
igraph_filter_vertex(): Subset an igraph to selected vertices
list2df(): list2df
load_all_msdev(): Load MSdev-related development packages
load_as_var(): Load RData File as Variable
load_demo(): Load bundled demo data objects
match_mz(): Match Ions by M/Z Only
match_mz_foverlaps(): Match m/z values using interval overlaps
match_mz_rt(): Match Ions by M/Z and Retention Time
matrixSub(): Matrix Subtraction of Two Vectors
median_part(): Extract Middle Portion of Vector
message_with_time(): Display Message with Timestamp
normalize_max_min(): Normalize Values Using Min-Max Scaling
open_dir(): Open Directory in File Explorer
open_plot_pdf(): open_plot_pdf
open_plot_ppt(): open_plot_ppt
open_plot_win(): open_plot_win
plot_Chromatograph_mirror(): Mirror plot of two chromatograms
plot_MSdev_feature_spectrum(): Plot MS/MS spectrum for a feature
plot_PCA(): Plot Principal Component Analysis (PCA)
plot_Spectra(): Plot Mass Spectra
plot_xcms_feature_group_EIC_comparasion(): Mirror EIC comparison grid for feature groups
plot_xcms_feature_group_similarity(): Heatmap of xcms feature-group EIC similarity
plotly_Spectra(): Create Interactive Plotly Mass Spectrum
plotly_Spectra_Ring_Artifact(): Interactive spectrum with click-locked reference peak
plotly_Spectra_iso_mirror(): Create Interactive Isotopic Mirror Plot
plotly_Spectra_mirror(): Create Interactive Mirror Plot of Two Spectra
setRStudioDir(): Set RStudio Files Pane Directory
setwdActivedFilePath(): setwdActivedFilePath
split_df(): Split Data Frame Randomly
analyzePathwayGlobalTest() analyzePathwayHyperTest(): analyzePathwayGlobalTest
str_short(): str_short
vector2str(): vector2str
write.xlsx(): Write data to Excel file
xcmsProcessingMS1(): xcmsProcessingMS1
xcmsProcessingMSdev.DDA(): Process DDA data using xcms
xcms_get_feature_ms1_candidate(): XCMS MS1 annotation helpers
get_xcms_Autotuner(): Get XCMS Parameters via Autotuner
get_xcms_chromatogram() get_xcms_peaks_chromatogram() get_xcms_feature_chromatogram() XChromatograms_rt_unit() XChromatograms_subset_feature() XChromatograms_fill_2point() plot_XChromatograms(): XCMS chromatogram helpers
get_xcms_feature_se() xcms_get_feature_def_stat(): XCMS feature helpers
xcms_get_feature_group(): Group xcms Features
xcms_get_feature_isotopologues() xcms_get_feature_isotopologues_multi_tracer() xcms_get_feature_traced_isotopologue() get_xcms_iso_fraction(): XCMS isotopologue helpers
plot_xcms_features_heatmap() plot_xcms_peaks_distribution() plot_xcms_features_distribution() plot_xcms_feature_chromatogram() plot_xcms_peaks_ms1_scans() plot_xcms_ms1_scan_freq() plot_xcms_peaks_ms2_scans() plot_xcms_peaks_Chromatogram() plot_xcms_feature_intensity() plot_xcms_TIC() plot_xcms_xic(): Heatmap of xcms feature intensities
xcms_get_dda_ms2_assignment(): xcms_get_dda_ms2_assignment
xcms_get_dda_scan_stimulate(): Stimulate DDA cycle and assign MS2 to feature
xcms_get_feature_isotope_label(): Xcms Get Feature Isotope Label (Deprecated)
xcms_get_feature_purity(): Store MS1 feature purity matrix in XcmsExperiment qdata
xcms_get_feature_wmean(): Update feature mz/rt using peak-intensity weighted means
xcms_group_feature_EIC(): Group xcms features by EIC similarity within RT tolerance
xlsx.write.list(): Write list of data frames to Excel