| Test if a file is an edata file | .is_edata |
| Identify All Biomolecules for Use in Normalization | all_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 object | applyFilt applyFilt.customFilt applyFilt.cvFilt applyFilt.imdanovaFilt applyFilt.moleculeFilt applyFilt.proteomicsFilt applyFilt.rmdFilt applyFilt.RNAFilt applyFilt.totalCountFilt |
| Create pmartR Object of Class isobaricpepData | as.isobaricpepData |
| Create pmartR Object of Class lipidData | as.lipidData |
| Create pmartR Object of Class metabData | as.metabData |
| Create a `multiData` object from multiple omicsData objects | as.multiData |
| Create pmartR Object of Class nmrData | as.nmrData |
| Create pmartR Object of Class pepData | as.pepData |
| Create pmartR Object of Class proData | as.proData |
| Create pmartR Object of Class seqData | as.seqData |
| Generate an object from omicsData and/or statRes objects to pass to trelliscope building functions | as.trelliData |
| Generate an object from edata to pass to trelliscope building functions | as.trelliData.edata |
| Runs BP-Quant | bpquant |
| bpquant_mod function | bpquant_mod |
| Combines two omicsData objects with identical sample information. | combine_omicsData |
| Combine technical replicates of an omicsData object | combine_techreps |
| Identify biomolecules with no missing values across samples | complete_mols |
| Compute Correlation matrix of biomolecule data | cor_result |
| Returns data frame with comparisons to be made | create_comparisonDF |
| Custom Filter Object | custom_filter |
| Creates custom sample names to be used in plots | custom_sampnames |
| Pooled Coefficient of Variation (CV) Filter Object | cv_filter |
| Wrapper for DESeq2 workflow | DESeq2_wrapper |
| Differential Expression for seqData | diffexp_seq |
| Reduce Dimension of Data for Exploratory Data Analysis | dim_reduction |
| Diagnostic plot for seqData | dispersion_est |
| Replace Values Equal to x with y | edata_replace |
| Creates a list of six Data Frames, one for each summarizing metric | edata_summary |
| Apply a Transformation to the Data | edata_transform |
| Wrapper for edgeR workflow | edgeR_wrapper |
| Basic survival analysis function | fit_surv |
| *DEPRECATED*: Fetch the check.names attribute | get_check_names |
| Return comparisons of statRes object | get_comparisons |
| Return data_class of statRes or trelliData object | get_data_class |
| Fetch the data_info attribute | get_data_info |
| Fetch the normalization status of the data | get_data_norm |
| Fetch the current data scale | get_data_scale |
| Fetch the original data scale | get_data_scale_orig |
| Fetch the e_data column name | get_edata_cname |
| Fetch the e_meta column name | get_emeta_cname |
| Fetch the f_data column name | get_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 attribute | get_filters |
| Fetch the group_DF attribute | get_group_DF |
| Get formula for group design | get_group_formula |
| Get group table | get_group_table |
| Fetch the isobaric_info attribute | get_isobaric_info |
| Fetch the isobaric normalization info | get_isobaric_norm |
| Compute the least squares means from a prediction grid and estimated coefficients | get_lsmeans |
| Fetch the meta_info attribute | get_meta_info |
| Fetch the nmr_info attribute | get_nmr_info |
| Fetch the NMR normalization info | get_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 test | group_comparison_anova |
| Group comparisons for the g-test | group_comparison_imd |
| Creates Attribute of omicsData Object for Group Membership | group_designation |
| Identifies biomolecules to be filtered out in preparation for IMD-ANOVA. | gtest_filter |
| Test for a qualitative and quantitative difference between groups using IMD and ANOVA, respectively | imd_anova |
| Tests for the independence of missing data across groups (aka factors, aka main effects) | imd_test |
| IMD-ANOVA Filter Object | imdanova_filter |
| Identify Biomolecules from the Top L Order Statistics for Use in Normalization | los |
| Median Absolute Deviation Transformation | mad_transform |
| Mean Center Transformation | mean_center |
| Median Center Transformation | median_center |
| Creates an object of class naRes (NA Result) | missingval_result |
| Molecule Filter Object | molecule_filter |
| Computes the Number of Non-Missing Data Points by Group | nonmissing_per_group |
| Calculate Normalization Parameters and Apply Global Normalization | normalize_global |
| Normalize e_data within SPANS | normalize_global_basic |
| Examine and Apply Isobaric Normalization | normalize_isobaric |
| Loess Normalization | normalize_loess |
| Normalize an Object of Class nmrData | normalize_nmr |
| Quantile Normalization | normalize_quantile |
| Scale from zero to one | normalize_zero_one_scaling |
| Test the location and scale parameters from a normalization procedure | normRes_tests |
| Adjust p-values for multiple comparisons | p_adjustment_anova |
| Basic survival analysis plot | plot_km |
| Plot corRes Object | plot.corRes |
| Plot customFilt Object | plot.customFilt |
| Plot cvFilt Object | plot.cvFilt |
| Plot dataRes object | plot.dataRes |
| Plot dimRes Object | plot.dimRes |
| Plot imdanovaFilt Object | plot.imdanovaFilt |
| Plot isobaricnormRes object | plot.isobaricnormRes |
| Plot isobaricpepData Object | plot.isobaricpepData |
| Plot lipidData Object | plot.lipidData |
| Plot metabData Object | plot.metabData |
| Plot moleculeFilt Object | plot.moleculeFilt |
| Plot naRes Object | plot.naRes |
| Plot nmrData Object | plot.nmrData |
| Plot nmrnormRes Object | plot.nmrnormRes |
| Plot normRes Object | plot.normRes |
| Plot pepData Object | plot.pepData |
| Plot proData Object | plot.proData |
| Plot proteomicsFilt Object | plot.proteomicsFilt |
| Plot rmdFilt Object | plot.rmdFilt |
| Plot RNAFilt Object | plot.RNAFilt |
| Plot seqData Object | plot.seqData |
| Plot SPANSRes Object | plot.SPANSRes |
| Plot statRes Object | plot.statRes |
| Plot totalCountFilt Object | plot.totalCountFilt |
| Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data | pmartR-package pmartR |
| Remove items that need to be filtered out | pmartR_filter_worker |
| Identify Biomolecules from the Proportion Present (PPP) for Use in Normalization | ppp |
| Identify Proportion of Peptides Present (PPP) and Rank Invariant Peptides (RIP) for Use in Normalization | ppp_rip |
| Protein Quantitation using Mean or Median Peptide Abundances | pquant |
| Create a Melted and Grouped Version of e_data for IMD_ANOVA filter | pre_imdanova_melt |
| Extract flag columns from a statRes object | prep_flags |
| print.customFilt | print.customFilt |
| Custom Filter Print Method | print.customFilterSummary |
| print.cvFilt | print.cvFilt |
| CV Filter Print Method | print.cvFilterSummary |
| print.dataRes | print.dataRes |
| print.imdanovaFilt | print.imdanovaFilt |
| IMD-ANOVA Filter Print Method | print.imdanovaFilterSummary |
| print.lipidData | print.lipidData |
| print.metabData | print.metabData |
| print.moleculeFilt | print.moleculeFilt |
| Molecule Filter Print Method | print.moleculeFilterSummary |
| print.normRes | print.normRes |
| print.pepData | print.pepData |
| print.proData | print.proData |
| print.proteomicsFilt | print.proteomicsFilt |
| Proteomics Filter Print Method | print.proteomicsFilterSummary |
| print.rmdFilt | print.rmdFilt |
| RMD Filter Print Method | print.rmdFilterSummary |
| print.RNAFilt | print.RNAFilt |
| RNA Filter Print Method | print.RNAFiltSummary |
| print.seqData | print.seqData |
| print.totalCountFilt | print.totalCountFilt |
| Total Count Filter Print Method | print.totalCountFiltSummary |
| Protein Quantification | protein_quant |
| Proteomics Filter Object | proteomics_filter |
| Applies qrollup function | qrollup |
| Replace NA with 0 | replace_nas |
| Replace 0 with NA | replace_zeros |
| Creates a data frame displaying multiple metrics | report_dataRes |
| Identify Rank-Invariant Biomolcules for Use in Normalization | rip |
| Conversion between log2(RMD) and p-value | rmd_conversion |
| Robust Mahalanobis Distance (RMD) Filter Object | rmd_filter |
| RNA Filter Object | RNA_filter |
| Applies rrollup function | rrollup |
| Calculate the Mean Correlation of a Sample with Respect to Group | run_group_meancor |
| Calculate the Kurtosis of Sample Runs | run_kurtosis |
| Calculate the Median Absolute Deviance (MAD) of Sample Runs | run_mad |
| Calculate the Fraction of Missing Data of Sample Runs | run_prop_missing |
| Calculate the Skewness of Sample Runs | run_skewness |
| *DEPRECATED*: Set check.names attribute of omicsData object | set_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 Methods | spans_procedure |
| Function to take raw output of `imd_anova` and create output for `statRes` object | statRes_output |
| Summary of statRes Object | statRes-class |
| Basic survival analysis summary | summary_km |
| Summary for isobaricnormRes Object | summary-isobaricnormRes summary.isobaricnormRes |
| Summary of nmrnormRes Object | summary-nmrnormRes summary.nmrnormRes |
| Produce a basic summary of a pmartR omicsData S3 Object | summary-omicsData summary.lipidData summary.metabData summary.nmrData summary.pepData summary.proData summary.seqData |
| Summary of pmartR Analysis Functions | summary-pmartR-results summary.corRes summary.dimRes summary.normRes summary.SPANSRes |
| Summarizes potential plotting options for a trelliData object | summary-trelliData summary.trelliData |
| Custom Filter Summary | summary.customFilt |
| Coefficient of Variation (CV) Filter Summary | summary.cvFilt |
| IMD-ANOVA Filter Summary | summary.imdanovaFilt |
| Molecule Filter Summary | summary.moleculeFilt |
| Proteomics Filter Summary | summary.proteomicsFilt |
| RMD Filter Summary | summary.rmdFilt |
| RNA Filter Summary | summary.RNAFilt |
| Total Count Filter Summary | summary.totalCountFilt |
| Create a "surv_DF" attribute so that survival analysis can be implemented. | surv_designation |
| Compute pairwise differences | take_diff |
| Total Count Filter Object | total_count_filter |
| Boxplot trelliscope building function for abundance data | trelli_abundance_boxplot |
| Heatmap trelliscope building function for abundance data | trelli_abundance_heatmap |
| Histogram trelliscope building function for abundance data | trelli_abundance_histogram |
| Bar chart trelliscope building function for fold_change | trelli_foldchange_bar |
| Boxplot trelliscope building function for fold_changes | trelli_foldchange_boxplot |
| Heatmap trelliscope building function for fold_change | trelli_foldchange_heatmap |
| Volcano trelliscope building function for fold_change | trelli_foldchange_volcano |
| Bar chart trelliscope building function for missing data | trelli_missingness_bar |
| Set the "panel_by" variable for a trelliData object | trelli_panel_by |
| Performs initial checks for trelliData objects | trelli_precheck |
| Filter a paneled trelliData object by a p-value | trelli_pvalue_filter |
| Boxplot trelliscope building function for RNA-seq data | trelli_rnaseq_boxplot |
| Heatmap trelliscope building function for RNA-seq data | trelli_rnaseq_heatmap |
| Histogram trelliscope building function for RNA-Seq data | trelli_rnaseq_histogram |
| Bar chart trelliscope building function for Non-Zero counts in RNA-seq data | trelli_rnaseq_nonzero_bar |
| Replace x with y for a single vector | vector_replace |
| Wrapper for limma-voom workflow | voom_wrapper |
| Zero to One scaling | zero_one_scale |
| Applies zrollup function | zrollup |
| Z-Score Transformation | zscore_transform |
