Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

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Documentation for package ‘pmartR’ version 2.4.4

• DESCRIPTION file.

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

-- 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_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

-- 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 peptides 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
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 --

zrollup	Applies zrollup function
zscore_transform	Z-Score Transformation

-- misc --

.is_edata

Test if a file is an edata file