Package: autonomics 1.15.10
Aditya Bhagwat
autonomics: Unified Statistical Modeling of Omics Data
This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs.
Authors:
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autonomics.pdf |autonomics.html✨
autonomics/json (API)
NEWS
| # Install 'autonomics' in R: |
| install.packages('autonomics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:autonomics-1.15.0(bioc 3.21)autonomics-1.14.6(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaredataimportpreprocessingdimensionreductionprincipalcomponentregressiondifferentialexpressiongenesetenrichmenttranscriptomicstranscriptiongeneexpressionrnaseqmicroarrayproteomicsmetabolomicsmassspectrometry
Last updated 2 days agofrom:4e75ec5eda. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win | ERROR | Nov 20 2024 |
| R-4.5-linux | NOTE | Nov 20 2024 |
| R-4.4-win | NOTE | Nov 20 2024 |
| R-4.4-mac | NOTE | Nov 20 2024 |
| R-4.3-win | NOTE | Nov 20 2024 |
| R-4.3-mac | NOTE | Nov 20 2024 |
Exports:.extract_effectsize_features.extract_fdr_features.extract_n_features.extract_p_features.extract_sign_features.fit_limma.merge.plot_survival.read_compounddiscoverer.read_diann_precursors.read_diann_proteingroups.read_maxquant_phosphosites.read_maxquant_proteingroups.read_metabolon.read_rectangles.read_rnaseq_bams.read_rnaseq_counts.read_somascan%<>%%>%ABBREV_TO_ORGNAMEabstract_fitabstractvarabstractvecadd_adjusted_pvaluesadd_assay_meansadd_facetvarsadd_opentargets_by_uniprotadd_pspadd_smilesaltenrichanalysisanalysis<-analyzeannotate_compounddiscovererannotate_maxquantannotate_uniprot_restassert_compounddiscoverer_outputassert_correlation_matrixassert_diann_reportassert_fastadtassert_fragpipe_tsvassert_is_fractionassert_is_valid_sumexpassert_maxquant_phosphositesassert_maxquant_proteingroupsassert_positive_numberassert_scalar_subsetassert_valid_formulaassert_weakly_positive_numberAUTONOMICS_DATASETSbetabinbiplotbiplot_correctionsbiplot_covariatesblock_varsblock2lmecbind_imputedcentercodecode_controlcode_deviationcode_deviation_firstcode_diffcode_diff_forwardcode_helmertcode_helmert_forwardcoefscollapse_incollapsed_entrezg_to_symbolCOMPOUNDDISCOVERER_PATTERNSCONTAMINANTSURLcontr.diffcontr.treatment.explicitcontrast_subgroup_colscontrast_subgroup_rowscount_incount_outcountscounts<-counts2cpmcounts2tpmcpmcpm<-cpm2countscreate_designdata.tableDATADIRdefault_coefsdefault_formuladefault_geomdefault_sfiledefault_subgroupvardemultiplexdequantifydequantify_compounddiscovererDIMREDDIMREDSUPERDIMREDUNdownfeaturesdownload_contaminantsdownload_datadownload_gtfdownload_mcclain21download_tcga_exampledt2mateffectdteffectmateffectsizemateffectvareffectvecenrichmentens2orgentrezg_to_symbolEXISTENCE_TO_NUMBERexp2extractextract_coef_featuresextract_rectanglefactor2logicalfclusterfcorfdatafdata<-fdistfdr2pfdrmatfdrvarfdrvecfdtfdt<-filter_exprs_replicated_in_some_subgroupfilter_featuresfilter_medoidfilter_samplesfitfit_limmafit_lmfit_lmefit_lmerfit_lmxfit_survivalfit_wilcoxonfitcoefsfitdtfitsFITSEPfitvarsfix_xlgenesflevelsfnamesfnames<-formula2lmformula2lmerformula2strfscaleftypefvaluesfvarsfvars<-genome_to_orgdbgroup_by_levelguess_compounddiscoverer_quantityguess_fitsepguess_maxquant_quantityguess_sephas_multiple_levelshdlproteinsimputeinf_to_nainvert_subgroupsinvnormis_collapsed_subsetis_compounddiscoverer_outputis_correlation_matrixis_diann_reportis_fastadtis_fileis_fractionis_fragpipe_tsvis_imputedis_imputed<-is_maxquant_phosphositesis_maxquant_proteingroupsis_positive_numberis_scalar_subsetis_sigis_valid_formulais_weakly_positive_numberkeep_connected_blockskeep_connected_featureskeep_replicated_featureslabel2indexldaLINMOD_ENGINESlist_fileslist2matloadingmatloadingslog2countslog2counts<-log2cpmlog2cpm<-log2diffslog2diffs<-log2proteinslog2proteins<-log2siteslog2sites<-log2tpmlog2tpm<-log2transformlogical2factormake_alpha_palettemake_colorsmake_volcano_dtmap_fvaluesmat2dtmatrix2sumexpMAXQUANT_PATTERNSmdsplotmerge_compounddiscoverermerge_fdatamerge_fdtmerge_ffilemerge_sample_excelmerge_sample_filemerge_sdatamerge_sdtmessage_dfminusinf_to_namodeldtmodelfeaturesmodelmatmodelvarmodelvecMSIGCOLLECTIONSHUMANMSIGCOLLECTIONSMOUSEMSIGDIRna_to_stringna_to_zeronan_to_nanfactorsno_nasOPENTARGETSDIRoplsorder_on_effectorder_on_pparse_maxquant_hdrspcapdtpercentilespg_to_canonicalpg_to_isoformsplot_contrast_vennplot_contrastogramplot_dataplot_densitiesplot_designplot_detectionsplot_exprsplot_exprs_per_coefplot_feature_boxplotsplot_feature_densitiesplot_feature_violinsplot_fit_summaryplot_heatmapplot_joint_densityplot_matrixplot_sample_boxplotsplot_sample_densitiesplot_sample_nasplot_sample_violinsplot_subgroup_nasplot_subgroup_pointsplot_subgroup_violinsplot_summarized_detectionsplot_summaryplot_survivalplot_vennplot_venn_heatmapplot_violinsplot_volcanoplspmatPPATTERNPRECURSOR_QUANTITYpreprocess_rnaseq_countspull_columnspvarpvecquantnormrandom_nasread_affymetrixread_compounddiscovererread_contaminantdtread_contaminantsread_diannread_diann_proteingroupsread_fragpiperead_maxquant_phosphositesread_maxquant_proteingroupsread_metabolonread_msigdtread_olinkread_phosphositesread_proteingroupsread_rectanglesread_rnaseq_bamsread_rnaseq_countsread_salmonread_somascanread_uniprotdtrecollapsereset_fitREVIEWED_TO_NUMBERrm_diann_contaminantsrm_missing_in_all_samplesrm_missing_in_some_samplesrm_singleton_samplesrm_unmatched_samplessampleid_valuesscaledlibsizesscorscorematscoressdatasdata<-sdistsdtsdt<-slevelssmasnamessnames<-split_extractsplit_extract_fixedsplit_extract_regexsplit_featuressplit_samplessplssscalestri_any_regexstri_detect_fixed_in_collapsedsubgroup_arraysubgroup_levelssubgroup_matrixsubgroup_valuessubtract_baselinesubtract_differencessubtract_pairssumexp_to_longdtsumexp_to_subrep_dtsumexp_to_tsvsumexp_to_widedtsumexplist_to_longdtsummarize_fitsvaluessvalues<-svarssvars<-systematic_nastag_featurestag_hdlproteinsTAXON_TO_ORGNAMEtaxon2orgtdtTESTStmattpmtpm<-tvartvectwofactor_sumexpuncollapseupfeaturesvaluesvalues<-varlevels_dont_clashvenn_detectsvsnweightsweights<-write_odswrite_xlXzero_to_nazscore
Dependencies:abindaffyaffyioaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerbitbit64blobcachemcellrangercliclustercodingMatricescolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyredgeRfansifarverfastmapfilelockfractionalgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2ggrepelgluegridExtragtablehmshttrIRangesisobandjsonlitelabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplogrpolyclippreprocessCoreprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreadxlrematchrlangRSQLiteS4ArraysS4VectorsscalesSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisLitevsnwithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract coefficient features | .extract_effectsize_features .extract_fdr_features .extract_n_features .extract_p_features .extract_sign_features extract_coef_features |
| Clean Merge | .merge |
| Read compound discoverer files as-is | .read_compounddiscoverer |
| Read compound discoverer masslist files as-is | .read_compounddiscoverer_masslist |
| Read diann | .read_diann_precursors .read_diann_proteingroups read_diann read_diann_proteingroups |
| Read proteingroups/phosphosites as-is | .read_maxquant_phosphosites .read_maxquant_proteingroups |
| Read metabolon xlsxfile | .read_metabolon read_metabolon |
| Read omics data from rectangular file | .read_rectangles read_rectangles |
| Read rnaseq counts/bams | .read_rnaseq_bams .read_rnaseq_counts read_rnaseq_bams read_rnaseq_counts |
| Read somascan adatfile | .read_somascan read_somascan |
| Abstract model fit | abstract_fit |
| Add adjusted pvalues | add_adjusted_pvalues add_adjusted_pvalues.data.table add_adjusted_pvalues.SummarizedExperiment |
| Add assay means | add_assay_means |
| Add facetvars | add_facetvars |
| Add opentargets annotations | add_opentargets_by_uniprot |
| Add psp | add_psp |
| Add smiles | add_smiles |
| Alternative Enrichment Analysis | altenrich |
| Get/set analysis | analysis analysis,SummarizedExperiment-method analysis<- analysis<-,SummarizedExperiment,list-method |
| Analyze | analyze |
| Read compound discoverer output | annotate_compounddiscoverer |
| Annotate maxquant | annotate_maxquant |
| Annotate uniprot/ensp | annotate_uniprot_rest |
| Assert that x is a valid SummarizedExperiment | assert_is_valid_sumexp |
| Data used in examples/vignette/tests/longtests | AUTONOMICS_DATASETS |
| Bin continuous variable | bin bin.character bin.factor bin.logical bin.numeric bin.SummarizedExperiment |
| Biplot | biplot |
| Biplot batch corrections | biplot_corrections |
| Biplot covariates | biplot_covariates |
| Put block in lme-compatible format | block2lme block2lme.character block2lme.formula block2lme.list block_vars formula2lm formula2lmer |
| Center samples | center |
| Contrast Code Factor | code code.data.table code.factor code_control code_deviation code_deviation_first code_diff code_diff_forward code_helmert code_helmert_forward contr.diff contr.treatment.explicit |
| Get coefs | coefs coefs.data.table coefs.factor coefs.SummarizedExperiment |
| Collapsed entrezg to genesymbol | collapsed_entrezg_to_symbol |
| compound discoverer quantity patterns | COMPOUNDDISCOVERER_PATTERNS |
| Contaminants URL | CONTAMINANTSURL |
| Row/Col contrasts | contrast_subgroup_cols contrast_subgroup_rows |
| Count/Collapse in/outside intersection | collapse_in collapse_in.character collapse_in.factor collapse_in.list count_in count_in.character count_in.factor count_in.list count_out count_out.character count_out.factor count_out.list |
| Get/Set counts | counts counts,SummarizedExperiment-method counts<- counts<-,SummarizedExperiment,matrix-method counts<-,SummarizedExperiment,NULL-method counts<-,SummarizedExperiment,numeric-method |
| Convert between counts and cpm/tpm | counts2cpm cpm2counts |
| counts to tpm | counts2tpm |
| Get/Set cpm | cpm cpm,SummarizedExperiment-method cpm<- cpm<-,SummarizedExperiment,matrix-method cpm<-,SummarizedExperiment,numeric-method |
| Create design matrix | create_design create_design.data.table create_design.SummarizedExperiment |
| Download autonomics example data | DATADIR download_data |
| Get default coefs | default_coefs default_coefs.data.table default_coefs.SummarizedExperiment |
| Default geom | default_geom |
| Default sfile | default_sfile |
| Create default formula | default_formula default_subgroupvar |
| Demultiplex snames | demultiplex |
| Dequantify maxquant snames | dequantify |
| dequantify_compounddiscoverer compound discoverer snames | dequantify_compounddiscoverer |
| Dimension Reduction Methods | DIMRED DIMREDSUPER DIMREDUN |
| Downloads contaminants | download_contaminants |
| Download GTF file | download_gtf |
| Download mcclain21 data | download_mcclain21 |
| Download tcga example | download_tcga_example |
| `data.table` to `matrix` | dt2mat mat2dt |
| Enrichment analysis | enrichment |
| taxon/ens to organism | ens2org taxon2org |
| Entrezg to genesymbol | entrezg_to_symbol |
| Extract rectangle from omics file, data.table, or matrix | extract_rectangle extract_rectangle.character extract_rectangle.data.table extract_rectangle.matrix |
| Cluster features | fcluster |
| Get/Set sample/feature data | fdata fdata,SummarizedExperiment-method fdata<- fdata<-,SummarizedExperiment,data.frame-method fdt fdt,SummarizedExperiment-method fdt<- fdt<-,SummarizedExperiment,data.table-method sdata sdata,SummarizedExperiment-method sdata<- sdata<-,SummarizedExperiment,data.frame-method sdata<-,SummarizedExperiment,DataFrame-method sdt sdt,SummarizedExperiment-method sdt<- sdt<-,SummarizedExperiment,data.table-method |
| fdr to p | fdr2p |
| Filter features with replicated expression in some subgroup | filter_exprs_replicated_in_some_subgroup |
| Filter features on condition | filter_features |
| Filter medoid sample | filter_medoid |
| Filter samples on condition | filter_samples |
| Fit General Linear Model | .fit_limma fit fit_limma fit_wilcoxon |
| Fit lm, lme, or lmer | fit_lm fit_lme fit_lmer fit_lmx |
| Fit/Plot survival | .plot_survival fit_survival plot_survival |
| fitcoefs | fitcoefs |
| Get fit models | fits fits.data.table fits.SummarizedExperiment |
| Fit results separator | FITSEP PPATTERN |
| Get fit vars/dt | fitdt fitvars |
| Fix excel genes | fix_xlgenes |
| Get fvar levels | flevels |
| Get/Set fnames | fnames fnames,SummarizedExperiment-method fnames<- fnames<-,SummarizedExperiment,character-method |
| formula to string | formula2str |
| Feature type | ftype |
| Get fvalues | fvalues |
| Get/Set fvars | fvars fvars,SummarizedExperiment-method fvars<- fvars<-,SummarizedExperiment,character-method |
| Get corresponding orgdb | genome_to_orgdb |
| group by level | group_by_level group_by_level.character group_by_level.data.table group_by_level.factor |
| Guess compound discoverer quantity from snames | guess_compounddiscoverer_quantity |
| guess fitsep | guess_fitsep guess_fitsep.data.table guess_fitsep.SummarizedExperiment |
| Guess maxquant quantity from snames | guess_maxquant_quantity |
| Guess separator | guess_sep guess_sep.character guess_sep.factor guess_sep.numeric guess_sep.SummarizedExperiment |
| Variable has multiple levels? | has_multiple_levels has_multiple_levels.character has_multiple_levels.data.table has_multiple_levels.factor has_multiple_levels.numeric has_multiple_levels.SummarizedExperiment |
| hdl proteomewatch proteins | hdlproteins |
| Impute | impute impute.matrix impute.numeric impute.SummarizedExperiment |
| Invert subgroups | invert_subgroups |
| Is collapsed subset | is_collapsed_subset |
| Assert correlation matrix | assert_correlation_matrix is_correlation_matrix |
| Is diann, fragpipe, proteingroups, phosphosites file? | assert_compounddiscoverer_output assert_diann_report assert_fragpipe_tsv assert_maxquant_phosphosites assert_maxquant_proteingroups is_compounddiscoverer_output is_diann_report is_fragpipe_tsv is_maxquant_phosphosites is_maxquant_proteingroups |
| Is fastadt | assert_fastadt is_fastadt |
| Is a file? | is_file |
| Is fraction | assert_is_fraction is_fraction |
| Get/set is_imputed | is_imputed is_imputed,SummarizedExperiment-method is_imputed<- is_imputed<-,SummarizedExperiment,matrix-method is_imputed<-,SummarizedExperiment,NULL-method |
| Is positive number | assert_positive_number assert_weakly_positive_number is_positive_number is_weakly_positive_number |
| Is scalar subset | assert_scalar_subset is_scalar_subset |
| Is significant? | is_sig |
| Is valid formula | assert_valid_formula is_valid_formula |
| Keep fully connected blocks | keep_connected_blocks |
| Keep features with n+ connected blocks | keep_connected_features |
| Keep replicated features | keep_replicated_features |
| Convert labels into indices | label2index |
| Linear Modeling Engines | LINMOD_ENGINES |
| list files | list_files |
| list to matrix | list2mat |
| Get/Set log2counts | log2counts log2counts,SummarizedExperiment-method log2counts<- log2counts<-,SummarizedExperiment,matrix-method log2counts<-,SummarizedExperiment,numeric-method |
| Get/Set log2cpm | log2cpm log2cpm,SummarizedExperiment-method log2cpm<- log2cpm<-,SummarizedExperiment,matrix-method log2cpm<-,SummarizedExperiment,numeric-method |
| Get/Set log2diffs | log2diffs log2diffs,SummarizedExperiment-method log2diffs<- log2diffs<-,SummarizedExperiment,matrix-method log2diffs<-,SummarizedExperiment,numeric-method |
| Get/Set log2proteins | log2proteins log2proteins,SummarizedExperiment-method log2proteins<- log2proteins<-,SummarizedExperiment,matrix-method log2proteins<-,SummarizedExperiment,numeric-method |
| Get/Set log2sites | log2sites log2sites,SummarizedExperiment-method log2sites<- log2sites<-,SummarizedExperiment,matrix-method log2sites<-,SummarizedExperiment,numeric-method |
| Get/Set log2tpm | log2tpm log2tpm,SummarizedExperiment-method log2tpm<- log2tpm<-,SummarizedExperiment,matrix-method log2tpm<-,SummarizedExperiment,numeric-method |
| Transform values | exp2 fscale invnorm log2transform quantnorm sscale vsn zscore |
| logical to factor | factor2logical logical2factor |
| Make alpha palette | make_alpha_palette |
| Make colors | make_colors |
| Create volcano datatable | make_volcano_dt |
| Map fvalues | map_fvalues |
| Convert matrix into SummarizedExperiment | matrix2sumexp |
| maxquant quantity patterns | MAXQUANT_PATTERNS |
| Feature correlations/distances | fcor fdist mdsplot scor sdist |
| merge compound discoverer files | merge_compounddiscoverer |
| Merge sample excel | merge_sample_excel |
| Merge sample / feature file | merge_ffile merge_sample_file |
| Merge sample/feature dt | merge_fdata merge_fdt merge_sdata merge_sdt |
| message dataframe | message_df |
| Get model variable | abstractvar abstractvar.data.table abstractvar.SummarizedExperiment abstractvec abstractvec.data.table abstractvec.SummarizedExperiment downfeatures effectdt effectmat effectsizemat effectvar effectvec fdrmat fdrvar fdrvec modeldt modeldt.data.table modeldt.SummarizedExperiment modelfeatures modelfeatures.data.table modelfeatures.SummarizedExperiment modelmat modelvar modelvar.data.table modelvar.SummarizedExperiment modelvec modelvec.data.table modelvec.SummarizedExperiment pdt pmat pvar pvec tdt tmat tvar tvec upfeatures |
| Human/Mouse Msigdb Collections | MSIGCOLLECTIONSHUMAN MSIGCOLLECTIONSMOUSE |
| local msigdb dir | MSIGDIR |
| stri_split and extract | nfactors split_extract split_extract_fixed split_extract_regex |
| opentargets dir | OPENTARGETSDIR |
| Order on p | order_on_effect order_on_p |
| PCA, SMA, LDA, PLS, SPLS, OPLS | lda opls pca pls sma spls |
| survival percentiles | percentiles |
| proteingroup to isoforms | pg_to_canonical pg_to_isoforms |
| Plot contrast venn | plot_contrast_venn |
| Plot contrastogram | plot_contrastogram |
| Plot data | plot_data |
| Plot sample/feature distributions | plot_densities plot_feature_densities plot_sample_densities |
| Plot model | plot_design |
| Plot missingness per sample / subgroup | plot_detections plot_sample_nas plot_subgroup_nas plot_summarized_detections |
| Plot exprs for coef | plot_exprs plot_feature_boxplots plot_sample_boxplots |
| Plot exprs per coef | plot_exprs_per_coef |
| Plot fit summary | plot_fit_summary |
| Plot heatmap | plot_heatmap |
| Plot joint density | plot_joint_density |
| Plot binary matrix | plot_matrix |
| Plot features | plot_subgroup_points |
| Plot summary | plot_summary |
| Plot venn | plot_venn |
| Plot venn heatmap | plot_venn_heatmap |
| Plot sample/feature violins | plot_feature_violins plot_sample_violins plot_subgroup_violins plot_violins |
| Plot volcano | plot_volcano |
| diann precursor quantity | PRECURSOR_QUANTITY |
| Preprocess RNAseq counts | preprocess_rnaseq_counts |
| Pull columns in a dataframe to the front | pull_columns |
| Read affymetrix microarray | read_affymetrix |
| Read compound discoverer output | read_compounddiscoverer |
| Read contaminants | read_contaminants |
| Read fragpipe | read_fragpipe |
| Read maxquant phosphosites | read_maxquant_phosphosites read_phosphosites |
| Read maxquant proteingroups | read_maxquant_proteingroups read_proteingroups |
| Read msigdb datatable | read_msigdt |
| Read olink file | read_olink |
| Read salmon | read_salmon |
| Read fasta hdrs | parse_maxquant_hdrs read_contaminantdt read_uniprotdt |
| Reset fit | reset_fit |
| Rm contaminants | rm_diann_contaminants |
| Rm features missing in some samples | rm_missing_in_all_samples rm_missing_in_some_samples |
| rm unmatched/singleton samples | rm_singleton_samples rm_unmatched_samples |
| Get tmm-scaled libsizes | scaledlibsizes |
| Extract scores/loadings | loadingmat loadings scoremat scores |
| Get slevels | slevels subgroup_levels |
| Get/Set snames | snames snames,SummarizedExperiment-method snames<- snames<-,SummarizedExperiment,character-method |
| Split samples | cbind_imputed split_features split_samples |
| Does any string have a regex | stri_any_regex |
| Detect fixed patterns in collapsed strings | stri_detect_fixed_in_collapsed |
| Get subgroup matrix | subgroup_array subgroup_matrix |
| Subtract baseline | subtract_baseline subtract_differences subtract_pairs |
| Write sumexp to tsv | sumexp_to_tsv |
| SummarizedExperiment to data.table | sumexp_to_longdt sumexp_to_subrep_dt sumexp_to_widedt |
| SummarizedExperiment list to long data.table | sumexplist_to_longdt |
| Summarize fit | summarize_fit summarize_fit.data.table summarize_fit.SummarizedExperiment |
| Get/Set svalues | sampleid_values subgroup_values svalues svalues<- svalues<-,SummarizedExperiment,character-method |
| Get/Set svars | svars svars,MultiAssayExperiment-method svars,SummarizedExperiment-method svars<- svars<-,MultiAssayExperiment,character-method svars<-,SummarizedExperiment,character-method |
| Is systematic/random/full NA | no_nas random_nas systematic_nas |
| Tag features | tag_features |
| Tag hdlproteins | tag_hdlproteins |
| Annotation Maps | ABBREV_TO_ORGNAME EXISTENCE_TO_NUMBER REVIEWED_TO_NUMBER TAXON_TO_ORGNAME |
| Statistical models supported in autonomics | TESTS |
| Get/Set tpm | tpm tpm,SummarizedExperiment-method tpm<- tpm<-,SummarizedExperiment,matrix-method tpm<-,SummarizedExperiment,numeric-method |
| twofactor sumexp | twofactor_sumexp |
| Uncollapse/Recollapse | recollapse uncollapse |
| Get/Set expr values | values values,SummarizedExperiment-method values<- values<-,SummarizedExperiment,matrix-method values<-,SummarizedExperiment,numeric-method |
| Are varlevels unique | varlevels_dont_clash varlevels_dont_clash.data.table varlevels_dont_clash.SummarizedExperiment |
| Venn detects | venn_detects |
| Get/Set weights | weights weights,SummarizedExperiment-method weights<- weights<-,SummarizedExperiment,matrix-method weights<-,SummarizedExperiment,NULL-method weights<-,SummarizedExperiment,numeric-method |
| Write xl/ods | write_ods write_xl |
| Model based prediction | beta X |
| Change nondetect representation | inf_to_na minusinf_to_na nan_to_na na_to_string na_to_zero zero_to_na |
