# Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

## Documentation for package ‘pmartR’ version 2.5.1

- DESCRIPTION file
- Package README

## Help Pages

A B C D E F G I L M N P Q R S T V Z misc

pmartR-package | Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

## -- A --

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
applyFilt.customFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.cvFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.imdanovaFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.moleculeFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.proteomicsFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.rmdFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.RNAFilt | Apply a S3 filter object to a pmartR S3 object
applyFilt.totalCountFilt | 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

## -- B --

bpquant | Runs BP-Quant
bpquant_mod | bpquant_mod function

## -- C --

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

## -- D --

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

## -- E --

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

## -- F --

fit_surv | Basic survival analysis function

## -- G --

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 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_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.

## -- I --

imdanova_filter | IMD-ANOVA Filter Object
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)

## -- L --

los | Identify Biomolecules from the Top L Order Statistics for Use in Normalization

## -- M --

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

## -- N --

nonmissing_per_group | Computes the Number of Non-Missing Data Points by Group
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
normRes_tests | Test the location and scale parameters from a normalization procedure

## -- P --

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.RNAFilt | Plot RNAFilt Object
plot.seqData | Plot seqData Object
plot.SPANSRes | Plot SPANSRes 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
prep_flags | Extract flag columns from a statRes object
pre_imdanova_melt | Create a Melted and Grouped Version of e_data for IMD_ANOVA filter
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
p_adjustment_anova | Adjust p-values for multiple comparisons

## -- Q --

qrollup | Applies qrollup function

## -- R --

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 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

## -- S --

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.corRes | Summary of pmartR Analysis Functions
summary.customFilt | Custom Filter Summary
summary.cvFilt | Coefficient of Variation (CV) Filter Summary
summary.dimRes | Summary of pmartR Analysis Functions
summary.imdanovaFilt | IMD-ANOVA Filter Summary
summary.isobaricnormRes | Summary for isobaricnormRes Object
summary.lipidData | Produce a basic summary of a pmartR omicsData S3 Object
summary.metabData | Produce a basic summary of a pmartR omicsData S3 Object
summary.moleculeFilt | Molecule Filter Summary
summary.nmrData | Produce a basic summary of a pmartR omicsData S3 Object
summary.nmrnormRes | Summary of nmrnormRes Object
summary.normRes | Summary of pmartR Analysis Functions
summary.pepData | Produce a basic summary of a pmartR omicsData S3 Object
summary.proData | Produce a basic summary of a pmartR omicsData S3 Object
summary.proteomicsFilt | Proteomics Filter Summary
summary.rmdFilt | RMD Filter Summary
summary.RNAFilt | RNA Filter Summary
summary.seqData | Produce a basic summary of a pmartR omicsData S3 Object
summary.SPANSRes | Summary of pmartR Analysis Functions
summary.totalCountFilt | Total Count Filter Summary
summary.trelliData | Summarizes potential plotting options for a trelliData object
summary_km | Basic survival analysis summary
surv_designation | Create a "surv_DF" attribute so that survival analysis can be implemented.

## -- T --

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

## -- V --

vector_replace | Replace x with y for a single vector
voom_wrapper | Wrapper for limma-voom workflow

## -- Z --

zero_one_scale | Zero to One scaling
zrollup | Applies zrollup function
zscore_transform | Z-Score Transformation

## -- misc --

.is_edata | Test if a file is an edata file