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