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-dataResPlots an object of class dataRes
plot-isobaricnormResPlots an object of class isobaricnormRes
plot_kmBasic survival analysis plot
plot-naResPlots an object of class naRes
plot-nmrnormResPlots an object of class nmrnormRes
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.cvFilterSummaryPrint method for summary of CV filter
print.imdanovaFilterSummaryPrint method for summary of imdanova filter
print.moleculeFilterSummaryPrint method for summary of molecule filter
print.proteomicsFilterSummaryPrint method for summary of proteomics filter
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.