Package: pmartR 2.4.6

Lisa Bramer

pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

Authors:Lisa Bramer [aut, cre], Kelly Stratton [aut], Daniel Claborne [aut], Evan Glasscock [ctb], Rachel Richardson [ctb], David Degnan [ctb], Evan Martin [ctb]

pmartR_2.4.6.tar.gz
pmartR_2.4.6.tar.gz(r-4.5-noble)pmartR_2.4.6.tar.gz(r-4.4-noble)
pmartR_2.4.6.tgz(r-4.4-emscripten)pmartR_2.4.6.tgz(r-4.3-emscripten)
pmartR.pdf |pmartR.html
pmartR/json (API)

# Install 'pmartR' in R:
install.packages('pmartR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pmartr/pmartr/issues

Pkgdown:https://pmartr.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

3.59 score 156 scripts 470 downloads 84 exports 58 dependencies

Last updated 2 months agofrom:2cb9adfed2. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-linux-x86_64OKNov 14 2024

Exports:%>%%dopar%applyFiltas.isobaricpepDataas.lipidDataas.metabDataas.multiDataas.nmrDataas.pepDataas.proDataas.seqDataas.trelliDataas.trelliData.edatabpquantcombine_lipidDatacombine_techrepscor_resultcreate_comparisonDFcustom_filtercustom_sampnamescv_filterdiffexp_seqdim_reductiondispersion_estedata_replaceedata_summaryedata_transformfit_survget_check_namesget_comparisonsget_data_classget_data_infoget_data_normget_data_scaleget_data_scale_origget_edata_cnameget_emeta_cnameget_fdata_cnameget_filtersget_group_DFget_group_tableget_isobaric_infoget_isobaric_normget_meta_infoget_nmr_infoget_nmr_normget_spans_paramsgroup_designationimd_anovaimdanova_filtermissingval_resultmolecule_filternormalize_globalnormalize_isobaricnormalize_loessnormalize_nmrnormalize_quantilenormalize_zero_one_scalingnormRes_testsplot_kmprotein_quantproteomics_filterreport_dataResrmd_conversionrmd_filterRNA_filterset_check_namesspans_proceduresummary_kmtotal_count_filtertrelli_abundance_boxplottrelli_abundance_heatmaptrelli_abundance_histogramtrelli_foldchange_bartrelli_foldchange_boxplottrelli_foldchange_heatmaptrelli_foldchange_volcanotrelli_missingness_bartrelli_panel_bytrelli_pvalue_filtertrelli_rnaseq_boxplottrelli_rnaseq_heatmaptrelli_rnaseq_histogramtrelli_rnaseq_nonzero_bar

Dependencies:BHBiobaseBiocGenericsclassclicodetoolscolorspacecpp11data.tableDEoptimRdoParalleldplyre1071fansifarverforeachgenericsggplot2glmpcagluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmeparallellypatchworkpcaMethodspcaPPpillarpkgconfigproxypurrrR6RColorBrewerRcppRcppArmadillorlangrobustbaserrcovscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Test if a file is an edata file.is_edata
Identify All Biomolecules for Use in Normalizationall_subset
Identifies biomolecules to be filtered in preparation for IMD-ANOVA.anova_filter
Tests for a quantiative difference between groups (aka factors, aka main effects)anova_test
Apply a S3 filter object to a pmartR S3 objectapplyFilt applyFilt.customFilt applyFilt.cvFilt applyFilt.imdanovaFilt applyFilt.moleculeFilt applyFilt.proteomicsFilt applyFilt.rmdFilt applyFilt.RNAFilt applyFilt.totalCountFilt
Create pmartR Object of Class isobaricpepDataas.isobaricpepData
Create pmartR Object of Class lipidDataas.lipidData
Create pmartR Object of Class metabDataas.metabData
Create a `multiData` object from multiple omicsData objectsas.multiData
Create pmartR Object of Class nmrDataas.nmrData
Create pmartR Object of Class pepDataas.pepData
Create pmartR Object of Class proDataas.proData
Create pmartR Object of Class seqDataas.seqData
Generate an object from omicsData and/or statRes objects to pass to trelliscope building functionsas.trelliData
Generate an object from edata to pass to trelliscope building functionsas.trelliData.edata
Runs BP-Quantbpquant
bpquant_mod functionbpquant_mod
Combines two omicsData objects with identical sample information.combine_lipidData
Combine technical replicates of an omicsData objectcombine_techreps
Identify biomolecules with no missing values across samplescomplete_mols
Compute Correlation matrix of biomolecule datacor_result
Returns data frame with comparisons to be madecreate_comparisonDF
Custom Filter Objectcustom_filter
Creates custom sample names to be used in plotscustom_sampnames
Pooled Coefficient of Variation (CV) Filter Objectcv_filter
Wrapper for DESeq2 workflowDESeq2_wrapper
Differential Expression for seqDatadiffexp_seq
Reduce Dimension of Data for Exploratory Data Analysisdim_reduction
Diagnostic plot for seqDatadispersion_est
Replace Values Equal to x with yedata_replace
Creates a list of six Data Frames, one for each summarizing metricedata_summary
Apply a Transformation to the Dataedata_transform
Wrapper for edgeR workflowedgeR_wrapper
Basic survival analysis functionfit_surv
*DEPRECATED*: Fetch the check.names attributeget_check_names
Return comparisons of statRes objectget_comparisons
Return data_class of statRes or trelliData objectget_data_class
Fetch the data_info attributeget_data_info
Fetch the normalization status of the dataget_data_norm
Fetch the current data scaleget_data_scale
Fetch the original data scaleget_data_scale_orig
Fetch the e_data column nameget_edata_cname
Fetch the e_meta column nameget_emeta_cname
Fetch the f_data column nameget_fdata_cname
Extracts the types of filters that have been applied. This function will be used at the beginning of the applyFilt function to give a warning if the same type of filter has already been applied.get_filter_type
Fetch the filters attributeget_filters
Fetch the group_DF attributeget_group_DF
Get formula for group designget_group_formula
Get group tableget_group_table
Fetch the isobaric_info attributeget_isobaric_info
Fetch the isobaric normalization infoget_isobaric_norm
Compute the least squares means from a prediction grid and estimated coefficientsget_lsmeans
Fetch the meta_info attributeget_meta_info
Fetch the nmr_info attributeget_nmr_info
Fetch the NMR normalization infoget_nmr_norm
Build the prediction grid to compute least squares means.get_pred_grid
Gets the parameters for the highest ranked methods from spans.get_spans_params
Group comparisons for the anova testgroup_comparison_anova
Group comparisons for the g-testgroup_comparison_imd
Creates Attribute of omicsData Object for Group Membershipgroup_designation
Identifies peptides to be filtered out in preparation for IMD-ANOVA.gtest_filter
Test for a qualitative and quantitative difference between groups using IMD and ANOVA, respectivelyimd_anova
Tests for the independence of missing data across groups (aka factors, aka main effects)imd_test
IMD-ANOVA Filter Objectimdanova_filter
Identify Biomolecules from the Top L Order Statistics for Use in Normalizationlos
Median Absolute Deviation Transformationmad_transform
Mean Center Transformationmean_center
Median Center Transformationmedian_center
Creates an object of class naRes (NA Result)missingval_result
Molecule Filter Objectmolecule_filter
Computes the Number of Non-Missing Data Points by Groupnonmissing_per_group
Calculate Normalization Parameters and Apply Global Normalizationnormalize_global
Normalize e_data within SPANSnormalize_global_basic
Examine and Apply Isobaric Normalizationnormalize_isobaric
Loess Normalizationnormalize_loess
Normalize an Object of Class nmrDatanormalize_nmr
Quantile Normalizationnormalize_quantile
Scale from zero to onenormalize_zero_one_scaling
Test the location and scale parameters from a normalization procedurenormRes_tests
Adjust p-values for multiple comparisonsp_adjustment_anova
Basic survival analysis plotplot_km
Plot corRes Objectplot.corRes
Plot customFilt Objectplot.customFilt
Plot cvFilt Objectplot.cvFilt
Plot dataRes objectplot.dataRes
Plot dimRes Objectplot.dimRes
Plot imdanovaFilt Objectplot.imdanovaFilt
Plot isobaricnormRes objectplot.isobaricnormRes
Plot isobaricpepData Objectplot.isobaricpepData
Plot lipidData Objectplot.lipidData
Plot metabData Objectplot.metabData
Plot moleculeFilt Objectplot.moleculeFilt
Plot naRes Objectplot.naRes
Plot nmrData Objectplot.nmrData
Plot nmrnormRes Objectplot.nmrnormRes
Plot normRes Objectplot.normRes
Plot pepData Objectplot.pepData
Plot proData Objectplot.proData
Plot proteomicsFilt Objectplot.proteomicsFilt
Plot rmdFilt Objectplot.rmdFilt
Plot RNAFilt Objectplot.RNAFilt
Plot seqData Objectplot.seqData
Plot SPANSRes Objectplot.SPANSRes
Plot statRes Objectplot.statRes
Plot totalCountFilt Objectplot.totalCountFilt
Panomics Marketplace - Quality Control and Statistical Analysis for Panomics DatapmartR
Remove items that need to be filtered outpmartR_filter_worker
Identify Biomolecules from the Proportion Present (PPP) for Use in Normalizationppp
Identify Proportion of Peptides Present (PPP) and Rank Invariant Peptides (RIP) for Use in Normalizationppp_rip
Protein Quantitation using Mean or Median Peptide Abundancespquant
Create a Melted and Grouped Version of e_data for IMD_ANOVA filterpre_imdanova_melt
Extract flag columns from a statRes objectprep_flags
print.customFiltprint.customFilt
Custom Filter Print Methodprint.customFilterSummary
print.cvFiltprint.cvFilt
CV Filter Print Methodprint.cvFilterSummary
print.dataResprint.dataRes
print.imdanovaFiltprint.imdanovaFilt
IMD-ANOVA Filter Print Methodprint.imdanovaFilterSummary
print.lipidDataprint.lipidData
print.metabDataprint.metabData
print.moleculeFiltprint.moleculeFilt
Molecule Filter Print Methodprint.moleculeFilterSummary
print.normResprint.normRes
print.pepDataprint.pepData
print.proDataprint.proData
print.proteomicsFiltprint.proteomicsFilt
Proteomics Filter Print Methodprint.proteomicsFilterSummary
print.rmdFiltprint.rmdFilt
RMD Filter Print Methodprint.rmdFilterSummary
print.RNAFiltprint.RNAFilt
RNA Filter Print Methodprint.RNAFiltSummary
print.seqDataprint.seqData
print.totalCountFiltprint.totalCountFilt
Total Count Filter Print Methodprint.totalCountFiltSummary
Protein Quantificationprotein_quant
Proteomics Filter Objectproteomics_filter
Applies qrollup functionqrollup
Replace NA with 0replace_nas
Replace 0 with NAreplace_zeros
Creates a data frame displaying multiple metricsreport_dataRes
Identify Rank-Invariant Biomolcules for Use in Normalizationrip
Conversion between log2(RMD) and p-valuermd_conversion
Robust Mahalanobis Distance (RMD) Filter Objectrmd_filter
RNA Filter ObjectRNA_filter
Applies rrollup functionrrollup
Calculate the Mean Correlation of a Sample with Respect to Grouprun_group_meancor
Calculate the Kurtosis of Sample Runsrun_kurtosis
Calculate the Median Absolute Deviance (MAD) of Sample Runsrun_mad
Calculate the Fraction of Missing Data of Sample Runsrun_prop_missing
Calculate the Skewness of Sample Runsrun_skewness
*DEPRECATED*: Set check.names attribute of omicsData objectset_check_names
Creates the list of median p-values used to make the background distribution used to compute the SPANS score in step 2.spans_make_distribution
Calculate SPANS Score for a Number of Normalization Methodsspans_procedure
Function to take raw output of `imd_anova` and create output for `statRes` objectstatRes_output
Summary of statRes ObjectstatRes-class
Basic survival analysis summarysummary_km
Summary for isobaricnormRes Objectsummary-isobaricnormRes summary.isobaricnormRes
Summary of nmrnormRes Objectsummary-nmrnormRes summary.nmrnormRes
Produce a basic summary of a pmartR omicsData S3 Objectsummary-omicsData summary.lipidData summary.metabData summary.nmrData summary.pepData summary.proData summary.seqData
Summary of pmartR Analysis Functionssummary-pmartR-results summary.corRes summary.dimRes summary.normRes summary.SPANSRes
Summarizes potential plotting options for a trelliData objectsummary-trelliData summary.trelliData
Custom Filter Summarysummary.customFilt
Coefficient of Variation (CV) Filter Summarysummary.cvFilt
IMD-ANOVA Filter Summarysummary.imdanovaFilt
Molecule Filter Summarysummary.moleculeFilt
Proteomics Filter Summarysummary.proteomicsFilt
RMD Filter Summarysummary.rmdFilt
RNA Filter Summarysummary.RNAFilt
Total Count Filter Summarysummary.totalCountFilt
Create a "surv_DF" attribute so that survival analysis can be implemented.surv_designation
Compute pairwise differencestake_diff
Total Count Filter Objecttotal_count_filter
Boxplot trelliscope building function for abundance datatrelli_abundance_boxplot
Heatmap trelliscope building function for abundance datatrelli_abundance_heatmap
Histogram trelliscope building function for abundance datatrelli_abundance_histogram
Bar chart trelliscope building function for fold_changetrelli_foldchange_bar
Boxplot trelliscope building function for fold_changestrelli_foldchange_boxplot
Heatmap trelliscope building function for fold_changetrelli_foldchange_heatmap
Volcano trelliscope building function for fold_changetrelli_foldchange_volcano
Bar chart trelliscope building function for missing datatrelli_missingness_bar
Set the "panel_by" variable for a trelliData objecttrelli_panel_by
Performs initial checks for trelliData objectstrelli_precheck
Filter a paneled trelliData object by a p-valuetrelli_pvalue_filter
Boxplot trelliscope building function for RNA-seq datatrelli_rnaseq_boxplot
Heatmap trelliscope building function for RNA-seq datatrelli_rnaseq_heatmap
Histogram trelliscope building function for RNA-Seq datatrelli_rnaseq_histogram
Bar chart trelliscope building function for Non-Zero counts in RNA-seq datatrelli_rnaseq_nonzero_bar
Replace x with y for a single vectorvector_replace
Wrapper for limma-voom workflowvoom_wrapper
Zero to One scalingzero_one_scale
Applies zrollup functionzrollup
Z-Score Transformationzscore_transform