All functions

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_lipidData()

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

.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 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 peptides 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(<totalCountFilt>)

Plot totalCountFilt Object

plot(<statRes>)

Plot statRes 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(<customFilt>)

print.customFilt

print(<cvFilt>)

print.cvFilt

print(<dataRes>)

print.dataRes

print(<imdanovaFilt>)

print.imdanovaFilt

print(<lipidData>)

print.lipidData

print(<metabData>)

print.metabData

print(<moleculeFilt>)

print.moleculeFilt

print(<normRes>)

print.normRes

print(<pepData>)

print.pepData

print(<proData>)

print.proData

print(<proteomicsFilt>)

print.proteomicsFilt

print(<rmdFilt>)

print.rmdFilt

print(<seqData>)

print.seqData

print(<totalCountFilt>)

print.totalCountFilt

print(<RNAFiltSummary>)

RNA Filter Print Method

print(<customFilterSummary>)

Custom Filter Print Method

print(<cvFilterSummary>)

CV Filter Print Method

print(<imdanovaFilterSummary>)

IMD-ANOVA Filter Print Method

print(<moleculeFilterSummary>)

Molecule Filter Print Method

print(<proteomicsFilterSummary>)

Proteomics Filter Print Method

print(<rmdFilterSummary>)

RMD Filter Print Method

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(<pepData>) summary(<proData>) summary(<lipidData>) summary(<metabData>) summary(<nmrData>) summary(<seqData>)

Produce a basic summary of a pmartR omicsData S3 Object

summary(<normRes>) summary(<SPANSRes>) summary(<dimRes>) summary(<corRes>)

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