Man pages for pmartR/pmartR
Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data
| all_subset | Identifies the 'subset' of All Features |
| analysis_log | Creates R markdown document report |
| 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 | Convert Data to Appropriate pmartR Class |
| as.lipidData | Convert Data to Appropriate pmartR Class |
| as.metabData | Convert Data to Appropriate pmartR Class |
| as.multiData | Create a 'multiData' object from multiple omicsData objects |
| as.nmrData | Convert Data to Appropriate pmartR Class |
| as.pepData | Convert Data to Appropriate pmartR Class |
| as.proData | Convert Data to Appropriate pmartR Class |
| bpquant | Runs BP-Quant |
| bpquant_mod | bpquant_mod function |
| combine_lipidData | 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 | Correlation matrix of biomolecule data |
| create_comparisonDF | Returns data.frame with comparisons to be made |
| custom_filter | Custom Filter |
| custom_sampnames | Creates custom sample names for plots |
| cv_filter | Filter Based on Pooled Coefficient of Variation (CV) Values |
| dim_reduction | Reduce Dimension of Data for Exploratory Data Analysis |
| 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 |
| 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 | Fetch the check.names attribute |
| get_comparisons | Return comparisons of statRes object |
| get_data_class | Return data_class of statRes or trellData 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_group_DF | Fetch the group_DF attribute |
| get_group_table | Get group table |
| get_isobaric_info | Fetch the isobaric_info attribute |
| get_isobaric_norm | Fetch the isobaric normalization info |
| 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_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 containing Group... |
| gtest_filter | Identifies peptides to be filtered out in preparation for... |
| gtest_heatmap | Plot a heatmap for the g-test results of imd-anova |
| hello | Hello, World! |
| imd_anova | Tests 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 Features from the Top L Order Statistics |
| 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 |
| molecule_filter | Molecule filter object |
| MSnSet2pepData | Convert Data of class MSnSet to pmartR pepData Class |
| nonmissing_per_group | Computes the Number of Non-Missing Data Points by Group |
| normalize_global | Calculate Normalization Parameters |
| normalize_global_basic | Normalize e_data within SPANS |
| normalize_isobaric | Normalize an object of class isobaricpepData |
| normalize_loess | Loess Normalization |
| normalize_nmr | Normalize an object of class nmrData |
| normalize_quantile | Quantile Normalization |
| normRes_tests | Test the location and scale parameters from a normalization... |
| p_adjustment_anova | Adjust p-values for multiple comparisons |
| plot-corRes | plot.corRes |
| plot-customFilt | plot.customFilt |
| plot-cvFilt | plot.cvFilt |
| plot-dataRes | Plots an object of class dataRes |
| plot-dimRes | plot.dimRes |
| plot-imdanovaFilt | plot.imdanovaFilt |
| plot-isobaricnormRes | Plots an object of class isobaricnormRes |
| plot-isobaricpepData | plot.isobaricpepData |
| plot_km | Basic survival analysis plot |
| plot-lipidData | plot.lipidData |
| plot-metabData | plot.metabData |
| plot-moleculeFilt | plot.moleculeFilt |
| plot-naRes | Plots an object of class naRes |
| plot-nmrData | plot.nmrData |
| plot-nmrnormRes | Plots an object of class nmrnormRes |
| plot-normRes | plot.normRes |
| plot-pepData | plot.pepData |
| plot-proData | plot.proData |
| plot-proteomicsFilt | plot.proteomicsFilt |
| plot-rmdFilt | plot.rmdFilt |
| plot-SPANSRes | Plots an object of class SPANSRes |
| plot.statRes | Plotting function for 'statRes' objects |
| pmartR | My package |
| pmartR_filter_worker | Remove items that need to be filtered out |
| ppp | Identify Proportion of the Peptides Present (PPP)... |
| 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-cvFilt | print.cvFilt |
| print.cvFilterSummary | Print method for summary of CV filter |
| print-dataRes | print.dataRes |
| print-imdanovaFilt | print.imdanovaFilt |
| print.imdanovaFilterSummary | Print method for summary of imdanova filter |
| print-lipidData | print.lipidData |
| print-metabData | print.metabData |
| print-moleculeFilt | print.moleculeFilt |
| print.moleculeFilterSummary | Print method for summary of molecule filter |
| print-normRes | print.normRes |
| print-pepData | print.pepData |
| print-proData | print.proData |
| print-proteomicsFilt | print.proteomicsFilt |
| print.proteomicsFilterSummary | Print method for summary of proteomics filter |
| print-rmdFilt | print.rmdFilt |
| protein_quant | protein_quant wrapper function |
| proteomics_filter | Proteomics filter object |
| qrollup | Applies qrollup function |
| reexports | Objects exported from other packages |
| replace_zeros | Replace 0 with NA |
| report_dataRes | Creates a data frame displaying multiple metrics |
| rip | Identify Rank-Invariant Peptides |
| rmd_conversion | Conversion between log2(RMD) and p-value |
| rmd_filter | RMD Runs |
| 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 | Set check.names attribute of omicsData object |
| 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 | statRes class. |
| 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 | Produce a basic summary of a custom_filter object |
| summary.cvFilt | Produce a basic summary of a cv_filter object |
| summary.imdanovaFilt | Produce a basic summary of a imdanova_filter object |
| summary-isobaricnormRes | Summarizes an object of class isobaricnormRes |
| summary_km | Basic survival analysis summary |
| summary.moleculeFilt | Produce a basic summary of a molecule_filter object |
| summary-nmrnormRes | Summarizes an object of class nmrnormRes |
| summary-omicsData | Produce a basic summary of a pmartR omicsData S3 Object |
| summary-pmartR-results | Produce summaries of various results objects from pmartR... |
| summary.proteomicsFilt | Produce a basic summary of a proteomics_filter object |
| summary.rmdFilt | Produce a basic summary of a rmd_filter object |
| surv_designation | Create a "surv_DF" attribute so that survival analysis can be... |
| take_diff | Compute pairwise differences |
| vector_replace | Replace x with y for a single vector |
| write_stat_results | Creates a list of three sheets, Normalized Data, DA Test... |
| write_stat_results_omics | Creates a list of three sheets, Normalized Data, DA Test... |
| zrollup | Applies zrollup function |
| zscore_transform | Z-Score Transformation |
