.is_edata               Test if a file is an edata file
DESeq2_wrapper          Wrapper for DESeq2 workflow
RNA_filter              RNA Filter Object
all_subset              Identify All Biomolecules for Use in
                        Normalization
anova_filter            Identifies biomolecules to be filtered in
                        preparation for IMD-ANOVA.
anova_test              Tests for a quantiative difference between
                        groups (aka factors, aka main effects)
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 pass to trelliscope building
                        functions
as.trelliData.edata     Generate an object from edata to pass to
                        trelliscope building functions
bpquant                 Runs BP-Quant
bpquant_mod             bpquant_mod function
combine_omicsData       Combines two omicsData objects with identical
                        sample information.
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
diffexp_seq             Differential Expression for seqData
dim_reduction           Reduce Dimension of Data for Exploratory Data
                        Analysis
dispersion_est          Diagnostic plot for seqData
edata_replace           Replace Values Equal to x with y
edata_summary           Creates a list of six Data Frames, one for each
                        summarizing metric
edata_transform         Apply a Transformation to the Data
edgeR_wrapper           Wrapper for edgeR workflow
fit_surv                Basic survival analysis function
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_filter_type         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_filters             Fetch the filters attribute
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 estimated coefficients
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 spans.
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 IMD-ANOVA.
imd_anova               Test for a qualitative and quantitative
                        difference between groups using IMD and ANOVA,
                        respectively
imd_test                Tests for the independence of missing data
                        across groups (aka factors, aka main effects)
imdanova_filter         IMD-ANOVA Filter Object
los                     Identify Biomolecules from the Top L Order
                        Statistics for Use in Normalization
mad_transform           Median Absolute Deviation Transformation
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
normRes_tests           Test the location and scale parameters from a
                        normalization procedure
normalize_global        Calculate Normalization Parameters and Apply
                        Global Normalization
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
p_adjustment_anova      Adjust p-values for multiple comparisons
plot.RNAFilt            Plot RNAFilt Object
plot.SPANSRes           Plot SPANSRes Object
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.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.seqData            Plot seqData Object
plot.statRes            Plot statRes Object
plot.totalCountFilt     Plot totalCountFilt Object
plot_km                 Basic survival analysis plot
pmartR                  Panomics Marketplace - Quality Control and
                        Statistical Analysis for Panomics Data
pmartR_filter_worker    Remove items that need to be filtered out
ppp                     Identify Biomolecules from the Proportion
                        Present (PPP) for Use in Normalization
ppp_rip                 Identify Proportion of Peptides Present (PPP)
                        and Rank Invariant Peptides (RIP) for Use in
                        Normalization
pquant                  Protein Quantitation using Mean or Median
                        Peptide Abundances
pre_imdanova_melt       Create a Melted and Grouped Version of e_data
                        for IMD_ANOVA filter
prep_flags              Extract flag columns from a statRes object
print.RNAFilt           print.RNAFilt
print.RNAFiltSummary    RNA Filter Print Method
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.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
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
rrollup                 Applies rrollup function
run_group_meancor       Calculate the Mean Correlation of a Sample with
                        Respect to Group
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
spans_make_distribution
                        Creates the list of median p-values used to
                        make the background distribution used to
                        compute the SPANS score in step 2.
spans_procedure         Calculate SPANS Score for a Number of
                        Normalization Methods
statRes-class           Summary of statRes Object
statRes_output          Function to take raw output of 'imd_anova' and
                        create output for 'statRes' object
summary-isobaricnormRes
                        Summary for isobaricnormRes Object
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-trelliData      Summarizes potential plotting options for a
                        trelliData object
summary.RNAFilt         RNA Filter Summary
summary.customFilt      Custom Filter Summary
summary.cvFilt          Coefficient of Variation (CV) Filter Summary
summary.imdanovaFilt    IMD-ANOVA Filter Summary
summary.moleculeFilt    Molecule Filter Summary
summary.proteomicsFilt
                        Proteomics Filter Summary
summary.rmdFilt         RMD Filter Summary
summary.totalCountFilt
                        Total Count Filter Summary
summary_km              Basic survival analysis summary
surv_designation        Create a "surv_DF" attribute so that survival
                        analysis can be implemented.
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 in RNA-seq data
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
