Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data
Identify All Biomolecules for Use in Normalization
Identifies biomolecules to be filtered in preparation for IMD-ANOVA.
Tests for a quantiative difference between groups (aka factors, aka ma...
Apply a S3 filter object to a pmartR S3 object
Create pmartR Object of Class isobaricpepData
Create pmartR Object of Class lipidData
Create pmartR Object of Class metabData
Create a multiData object from multiple omicsData objects
Create pmartR Object of Class nmrData
Create pmartR Object of Class pepData
Create pmartR Object of Class proData
Create pmartR Object of Class seqData
Generate an object from edata to pass to trelliscope building function...
Generate an object from omicsData and/or statRes objects to pass to tr...
bpquant_mod function
Runs BP-Quant
Helper to find the names of columns of a data.frame that contain exact...
Combines two omicsData objects with identical sample information.
Combine technical replicates of an omicsData object
Identify biomolecules with no missing values across samples
Compute Correlation matrix of biomolecule data
Returns data frame with comparisons to be made
Custom Filter Object
Creates custom sample names to be used in plots
Pooled Coefficient of Variation (CV) Filter Object
Wrapper for DESeq2 workflow
Differential Expression for seqData
Reduce Dimension of Data for Exploratory Data Analysis
Diagnostic plot for seqData
Test if a file is an edata file
Replace Values Equal to x with y
Creates a list of six Data Frames, one for each summarizing metric
Apply a Transformation to the Data
Wrapper for edgeR workflow
Find column names in f_meta for each object. May return in two objects...
Basic survival analysis function
Check that the f_meta file contains a column aligned to each omicsData...
DEPRECATED : Fetch the check.names attribute
Return comparisons of statRes object
Return data_class of statRes or trelliData object
Fetch the data_info attribute
Fetch the normalization status of the data
Fetch the original data scale
Fetch the current data scale
Fetch the e_data column name
Fetch the e_meta column name
Fetch the f_data column name
Extracts the types of filters that have been applied. This function wi...
Fetch the filters attribute
Fetch the group_DF attribute
Get formula for group design
Get group table
Fetch the isobaric_info attribute
Fetch the isobaric normalization info
Compute the least squares means from a prediction grid and estimated c...
Fetch the meta_info attribute
Fetch the nmr_info attribute
Fetch the NMR normalization info
Build the prediction grid to compute least squares means.
Gets the parameters for the highest ranked methods from spans.
Group comparisons for the anova test
Group comparisons for the g-test
Creates Attribute of omicsData Object for Group Membership
Identifies biomolecules to be filtered out in preparation for IMD-ANOV...
Plot a heatmap for the g-test results of imd-anova
Test for a qualitative and quantitative difference between groups usin...
Tests for the independence of missing data across groups (aka factors,...
IMD-ANOVA Filter Object
Identify Biomolecules from the Top L Order Statistics for Use in Norma...
Median Absolute Deviation Transformation
Create a plotting dataframe for volcano plots and heatmaps
Mean Center Transformation
Median Center Transformation
Creates an object of class naRes (NA Result)
Molecule Filter Object
Computes the Number of Non-Missing Data Points by Group
Normalize e_data within SPANS
Calculate Normalization Parameters and Apply Global Normalization
Examine and Apply Isobaric Normalization
Loess Normalization
Normalize an Object of Class nmrData
Quantile Normalization
Scale from zero to one
Test the location and scale parameters from a normalization procedure
Adjust p-values for multiple comparisons
Basic survival analysis plot
Plot corRes Object
Plot customFilt Object
Plot cvFilt Object
Plot dataRes object
Plot dimRes Object
Plot imdanovaFilt Object
Plot isobaricnormRes object
Plot isobaricpepData Object
Plot lipidData Object
Plot metabData Object
Plot moleculeFilt Object
Plot naRes Object
Plot nmrData Object
Plot nmrnormRes Object
Plot normRes Object
Plot pepData Object
Plot proData Object
Plot proteomicsFilt Object
Plot rmdFilt Object
Plot RNAFilt Object
Plot seqData Object
Plot SPANSRes Object
Plot totalCountFilt Object
Plot statRes Object
Remove items that need to be filtered out
Panomics Marketplace - Quality Control and Statistical Analysis for Pa...
Identify Proportion of Peptides Present (PPP) and Rank Invariant Pepti...
Identify Biomolecules from the Proportion Present (PPP) for Use in Nor...
Protein Quantitation using Mean or Median Peptide Abundances
Create a Melted and Grouped Version of e_data for IMD_ANOVA filter
Extract flag columns from a statRes object
print.customFilt
print.cvFilt
print.dataRes
print.imdanovaFilt
print.lipidData
print.metabData
print.moleculeFilt
print.normRes
print.pepData
print.proData
print.proteomicsFilt
print.rmdFilt
print.RNAFilt
print.seqData
print.totalCountFilt
Custom Filter Print Method
CV Filter Print Method
IMD-ANOVA Filter Print Method
Molecule Filter Print Method
Proteomics Filter Print Method
RMD Filter Print Method
RNA Filter Print Method
Total Count Filter Print Method
Protein Quantification
Proteomics Filter Object
Applies qrollup function
Objects exported from other packages
Replace NA with 0
Replace 0 with NA
Creates a data frame displaying multiple metrics
Identify Rank-Invariant Biomolcules for Use in Normalization
Conversion between log2(RMD) and p-value
Robust Mahalanobis Distance (RMD) Filter Object
RNA Filter Object
Applies rrollup function
Calculate the Mean Correlation of a Sample with Respect to Group
Calculate the Kurtosis of Sample Runs
Calculate the Median Absolute Deviance (MAD) of Sample Runs
Calculate the Fraction of Missing Data of Sample Runs
Calculate the Skewness of Sample Runs
DEPRECATED : Set check.names attribute of omicsData object
Functions to set omicsData attributes --------------------------------...
Sets/updates the filters attribute with a filter class object.
Sets/updates the values in the isobaric_info attribute.
Sets/updates the values in the meta_info attribute
Sets/updates the values in the nmr_info attribute.
Creates the list of median p-values used to make the background distri...
Calculate SPANS Score for a Number of Normalization Methods
Fold change barplots for statres objects
Fold change histogram for statres objects
Function to take raw output of imd_anova and create output for `stat...
Volcano plot for the anova results of imd-anova
Summary of statRes Object
Basic survival analysis summary
Summary for isobaricnormRes Object
Summary of nmrnormRes Object
Produce a basic summary of a pmartR omicsData S3 Object
Summary of pmartR Analysis Functions
Summarizes potential plotting options for a trelliData object
Custom Filter Summary
Coefficient of Variation (CV) Filter Summary
IMD-ANOVA Filter Summary
Molecule Filter Summary
Proteomics Filter Summary
RMD Filter Summary
RNA Filter Summary
Total Count Filter Summary
Create a "surv_DF" attribute so that survival analysis can be implemen...
Compute pairwise differences
Total Count Filter Object
Boxplot trelliscope building function for abundance data
Heatmap trelliscope building function for abundance data
Histogram trelliscope building function for abundance data
Bar chart trelliscope building function for fold_change
Boxplot trelliscope building function for fold_changes
Heatmap trelliscope building function for fold_change
Volcano trelliscope building function for fold_change
Bar chart trelliscope building function for missing data
Set the "panel_by" variable for a trelliData object
Performs initial checks for trelliData objects
Filter a paneled trelliData object by a p-value
Boxplot trelliscope building function for RNA-seq data
Heatmap trelliscope building function for RNA-seq data
Histogram trelliscope building function for RNA-Seq data
Bar chart trelliscope building function for Non-Zero counts in RNA-seq...
Replace x with y for a single vector
Wrapper for limma-voom workflow
Zero to One scaling
Applies zrollup function
Z-Score Transformation
Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.
Useful links