Man pages for pmartR/pmartR
Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

all_subsetIdentifies the 'subset' of All Features
analysis_logCreates R markdown document report
anova_filterIdentifies biomolecules to be filtered in preparation for...
anova_testTests for a quantiative difference between groups (aka...
applyFiltApply a S3 filter object to a pmartR S3 object
as.isobaricpepDataConvert Data to Appropriate pmartR Class
as.lipidDataConvert Data to Appropriate pmartR Class
as.metabDataConvert Data to Appropriate pmartR Class
as.multiDataCreate a 'multiData' object from multiple omicsData objects
as.nmrDataConvert Data to Appropriate pmartR Class
as.pepDataConvert Data to Appropriate pmartR Class
as.proDataConvert Data to Appropriate pmartR Class
bpquantRuns BP-Quant
bpquant_modbpquant_mod function
combine_lipidDataCombines two omicsData objects with identical sample...
combine_techrepsCombine technical replicates of an omicsData object
complete_molsIdentify biomolecules with no missing values across samples
cor_resultCorrelation matrix of biomolecule data
create_comparisonDFReturns data.frame with comparisons to be made
custom_filterCustom Filter
custom_sampnamesCreates custom sample names for plots
cv_filterFilter Based on Pooled Coefficient of Variation (CV) Values
dim_reductionReduce Dimension of Data for Exploratory Data Analysis
edata_replaceReplace Values Equal to x with y
edata_summaryCreates a list of six Data Frames, one for each summarizing...
edata_transformApply a Transformation to the Data
find_fmeta_cnamesFind column names in f_meta for each object. May return in...
fit_survBasic survival analysis function
fmeta_matchesCheck that the f_meta file contains a column aligned to each...
get_check_namesFetch the check.names attribute
get_comparisonsReturn comparisons of statRes object
get_data_classReturn data_class of statRes or trellData object
get_data_infoFetch the data_info attribute
get_data_normFetch the normalization status of the data
get_data_scaleFetch the current data scale
get_data_scale_origFetch the original data scale
get_edata_cnameFetch the e_data column name
get_emeta_cnameFetch the e_meta column name
get_fdata_cnameFetch the f_data column name
get_filtersFetch the filters attribute
get_group_DFFetch the group_DF attribute
get_group_tableGet group table
get_isobaric_infoFetch the isobaric_info attribute
get_isobaric_normFetch the isobaric normalization info
get_meta_infoFetch the meta_info attribute
get_nmr_infoFetch the nmr_info attribute
get_nmr_normFetch the NMR normalization info
get_spans_paramsGets the parameters for the highest ranked methods from...
group_comparison_anovaGroup comparisons for the anova test
group_comparison_imdGroup comparisons for the g-test
group_designationCreates Attribute of omicsData object containing Group...
gtest_filterIdentifies peptides to be filtered out in preparation for...
gtest_heatmapPlot a heatmap for the g-test results of imd-anova
helloHello, World!
imd_anovaTests for a qualitative and quantitative difference between...
imdanova_filterIMD-ANOVA filter object
imd_testTests for the independence of missing data across groups (aka...
losIdentify Features from the Top L Order Statistics
mad_transformMedian Absolute Deviation Transformation
make_volcano_plot_dfCreate a plotting dataframe for volcano plots and heatmaps.
mean_centerMean Center Transformation
median_centerMedian Center Transformation
missingval_resultCreates an object of class naRes
molecule_filterMolecule filter object
MSnSet2pepDataConvert Data of class MSnSet to pmartR pepData Class
nonmissing_per_groupComputes the Number of Non-Missing Data Points by Group
normalize_globalCalculate Normalization Parameters
normalize_global_basicNormalize e_data within SPANS
normalize_isobaricNormalize an object of class isobaricpepData
normalize_loessLoess Normalization
normalize_nmrNormalize an object of class nmrData
normalize_quantileQuantile Normalization
normRes_testsTest the location and scale parameters from a normalization...
p_adjustment_anovaAdjust p-values for multiple comparisons
plot-corResplot.corRes
plot-customFiltplot.customFilt
plot-cvFiltplot.cvFilt
plot-dataResPlots an object of class dataRes
plot-dimResplot.dimRes
plot-imdanovaFiltplot.imdanovaFilt
plot-isobaricnormResPlots an object of class isobaricnormRes
plot-isobaricpepDataplot.isobaricpepData
plot_kmBasic survival analysis plot
plot-lipidDataplot.lipidData
plot-metabDataplot.metabData
plot-moleculeFiltplot.moleculeFilt
plot-naResPlots an object of class naRes
plot-nmrDataplot.nmrData
plot-nmrnormResPlots an object of class nmrnormRes
plot-normResplot.normRes
plot-pepDataplot.pepData
plot-proDataplot.proData
plot-proteomicsFiltplot.proteomicsFilt
plot-rmdFiltplot.rmdFilt
plot-SPANSResPlots an object of class SPANSRes
plot.statResPlotting function for 'statRes' objects
pmartRMy package
pmartR_filter_workerRemove items that need to be filtered out
pppIdentify Proportion of the Peptides Present (PPP)...
ppp_ripIdentify Proportion of Peptides Present (PPP) and Rank...
pquantProtein Quantitation using Mean or Median Peptide Abundances
pre_imdanova_meltCreate a Melted and Grouped Version of e_data for IMD_ANOVA...
prep_flagsExtract flag columns from a statRes object
print-customFiltprint.customFilt
print-cvFiltprint.cvFilt
print.cvFilterSummaryPrint method for summary of CV filter
print-dataResprint.dataRes
print-imdanovaFiltprint.imdanovaFilt
print.imdanovaFilterSummaryPrint method for summary of imdanova filter
print-lipidDataprint.lipidData
print-metabDataprint.metabData
print-moleculeFiltprint.moleculeFilt
print.moleculeFilterSummaryPrint method for summary of molecule filter
print-normResprint.normRes
print-pepDataprint.pepData
print-proDataprint.proData
print-proteomicsFiltprint.proteomicsFilt
print.proteomicsFilterSummaryPrint method for summary of proteomics filter
print-rmdFiltprint.rmdFilt
protein_quantprotein_quant wrapper function
proteomics_filterProteomics filter object
qrollupApplies qrollup function
reexportsObjects exported from other packages
replace_zerosReplace 0 with NA
report_dataResCreates a data frame displaying multiple metrics
ripIdentify Rank-Invariant Peptides
rmd_conversionConversion between log2(RMD) and p-value
rmd_filterRMD Runs
rrollupApplies rrollup function
run_group_meancorCalculate the Mean Correlation of a Sample with Respect to...
run_kurtosisCalculate the Kurtosis of Sample Runs
run_madCalculate the Median Absolute Deviance (MAD) of Sample Runs
run_prop_missingCalculate the Fraction of Missing Data of Sample Runs
run_skewnessCalculate the Skewness of Sample Runs
set_check_namesSet check.names attribute of omicsData object
spans_make_distributionCreates the list of median p-values used to make the...
spans_procedureCalculate SPANS Score for a Number of Normalization Methods
statres_barplotFold change barplots for statres objects
statRes-classstatRes class.
statRes_outputFunction to take raw output of 'imd_anova' and create output...
statres_volcano_plotVolcano plot for the anova results of imd-anova
summary.customFiltProduce a basic summary of a custom_filter object
summary.cvFiltProduce a basic summary of a cv_filter object
summary.imdanovaFiltProduce a basic summary of a imdanova_filter object
summary-isobaricnormResSummarizes an object of class isobaricnormRes
summary_kmBasic survival analysis summary
summary.moleculeFiltProduce a basic summary of a molecule_filter object
summary-nmrnormResSummarizes an object of class nmrnormRes
summary-omicsDataProduce a basic summary of a pmartR omicsData S3 Object
summary-pmartR-resultsProduce summaries of various results objects from pmartR...
summary.proteomicsFiltProduce a basic summary of a proteomics_filter object
summary.rmdFiltProduce a basic summary of a rmd_filter object
surv_designationCreate a "surv_DF" attribute so that survival analysis can be...
take_diffCompute pairwise differences
vector_replaceReplace x with y for a single vector
write_stat_resultsCreates a list of three sheets, Normalized Data, DA Test...
write_stat_results_omicsCreates a list of three sheets, Normalized Data, DA Test...
zrollupApplies zrollup function
zscore_transformZ-Score Transformation
pmartR/pmartR documentation built on June 27, 2022, 10:35 p.m.