Generifying and intuifying cross-platform omics analysis
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Documentation for package ‘autonomics’ version 1.10.2
Help Pages
A B C D E F G H I L M N O P Q R S T V W Z misc
-- A --
| add_smiles | Add smiles |
| analysis | Get/set analysis |
| analysis-method | Get/set analysis |
| analysis<- | Get/set analysis |
| analysis<--method | Get/set analysis |
| analyze | Analyze |
| assert_is_valid_sumexp | Assert that x is a valid SummarizedExperiment |
| AUTONOMICS_DATASETS | Data used in examples/vignette/tests/longtests |
-- B --
| biplot | Biplot |
| biplot_corrections | Biplot batch corrections |
| biplot_covariates | Biplot covariates |
-- C --
| center | Center samples |
| contrastdefs | Get/set contrastdefs |
| contrastdefs-method | Get/set contrastdefs |
| contrastdefs<- | Get/set contrastdefs |
| contrastdefs<--method | Get/set contrastdefs |
| contrast_subgroup_cols | Row/Col contrasts |
| contrast_subgroup_rows | Row/Col contrasts |
| counts | Get/Set counts |
| counts-method | Get/Set counts |
| counts2cpm | Convert between counts and cpm |
| counts2tpm | counts to tpm |
| counts<- | Get/Set counts |
| counts<--method | Get/Set counts |
| cpm | Get/Set cpm |
| cpm-method | Get/Set cpm |
| cpm2counts | Convert between counts and cpm |
| cpm<- | Get/Set cpm |
| cpm<--method | Get/Set cpm |
| create_design | Create design |
| create_sfile | Create sfile |
-- D --
| default_formula | Create default formula |
| default_sfile | Default sfile |
| default_subgroupvar | Create default formula |
| download_data | Download autonomics example data |
| download_gtf | Download GTF file |
| dt2mat | 'data.table' to 'matrix' |
-- E --
| exp2 | Transform values |
| explore_imputations | Explore imputations |
| explore_transformations | Explore transformations |
| extract_features | Extract features |
| extract_rectangle | Extract rectangle from omics file, data.table, or matrix |
| extract_rectangle.character | Extract rectangle from omics file, data.table, or matrix |
| extract_rectangle.data.table | Extract rectangle from omics file, data.table, or matrix |
| extract_rectangle.matrix | Extract rectangle from omics file, data.table, or matrix |
-- F --
| fdata | Get/Set fdata |
| fdata-method | Get/Set fdata |
| fdata<- | Get/Set fdata |
| fdata<--method | Get/Set fdata |
| filter_exprs_replicated_in_some_subgroup | Filter features with replicated expression in some subgroup |
| filter_features | Filter features on condition |
| filter_medoid | Filter medoid sample |
| filter_replicated | Filter for replicated features |
| filter_samples | Filter samples on condition |
| fit_limma | Fit model and test for differential expression |
| fit_lm | Fit model and test for differential expression |
| fit_lme | Fit model and test for differential expression |
| fit_lmer | Fit model and test for differential expression |
| fit_wilcoxon | Fit model and test for differential expression |
| flevels | Get fvar levels |
| fnames | Get/Set fnames |
| fnames-method | Get/Set fnames |
| fnames<- | Get/Set fnames |
| fnames<--method | Get/Set fnames |
| formula2str | formula to string |
| fvalues | Get fvalues |
| fvars | Get/Set fvars |
| fvars-method | Get/Set fvars |
| fvars<- | Get/Set fvars |
| fvars<--method | Get/Set fvars |
-- G --
| guess_maxquant_quantity | Guess maxquant quantity from snames |
| guess_maxquant_quantity.character | Guess maxquant quantity from snames |
| guess_maxquant_quantity.data.frame | Guess maxquant quantity from snames |
| guess_maxquant_quantity.SummarizedExperiment | Guess maxquant quantity from snames |
| guess_sep | Guess separator |
| guess_sep.character | Guess separator |
| guess_sep.factor | Guess separator |
| guess_sep.SummarizedExperiment | Guess separator |
-- H --
| halfnormimpute | Impute from half-normal distribution around 0 |
-- I --
| impute_systematic_nondetects | Impute systematic nondetects |
| inf_to_na | Change nondetect representation |
| invert | Invert |
| invert.character | Invert |
| invert.SummarizedExperiment | Invert |
| invnorm | Transform values |
| is_imputed | Get/set is_imputed |
| is_imputed-method | Get/set is_imputed |
| is_imputed<- | Get/set is_imputed |
| is_imputed<--method | Get/set is_imputed |
| is_sig | Is significant? |
-- L --
| lda | Add PCA, SMA, LDA, PLS |
| limma | Get/set limma results |
| limma-method | Get/set limma results |
| limma<- | Get/set limma results |
| limma<--method | Get/set limma results |
| log2counts | Get/Set log2counts |
| log2counts-method | Get/Set log2counts |
| log2counts<- | Get/Set log2counts |
| log2counts<--method | Get/Set log2counts |
| log2countsratios | Get/Set log2countsratios |
| log2countsratios-method | Get/Set log2countsratios |
| log2countsratios<- | Get/Set log2countsratios |
| log2countsratios<--method | Get/Set log2countsratios |
| log2cpm | Get/Set log2cpm |
| log2cpm-method | Get/Set log2cpm |
| log2cpm<- | Get/Set log2cpm |
| log2cpm<--method | Get/Set log2cpm |
| log2cpmratios | Get/Set log2cpmratios |
| log2cpmratios-method | Get/Set log2cpmratios |
| log2cpmratios<- | Get/Set log2cpmratios |
| log2cpmratios<--method | Get/Set log2cpmratios |
| log2tpm | Get/Set log2tpm |
| log2tpm-method | Get/Set log2tpm |
| log2tpm<- | Get/Set log2tpm |
| log2tpm<--method | Get/Set log2tpm |
| log2tpmratios | Get/Set log2tpmratios |
| log2tpmratios-method | Get/Set log2tpmratios |
| log2tpmratios<- | Get/Set log2tpmratios |
| log2tpmratios<--method | Get/Set log2tpmratios |
| log2transform | Transform values |
-- M --
| make_volcano_dt | Create volcano datatable |
| mat2dt | 'data.table' to 'matrix' |
| matrix2sumexp | Convert matrix into SummarizedExperiment |
| MAXQUANT_PATTERNS_PEPCOUNTS | maxquant peptide count patterns |
| MAXQUANT_PATTERNS_QUANTITY | maxquant quantity patterns |
| merge_fdata | Merge sample/feature data |
| merge_ffile | Merge sample/feature file |
| merge_sdata | Merge sample/feature data |
| merge_sfile | Merge sample/feature file |
| message_df | message dataframe |
| minusinf_to_na | Change nondetect representation |
-- N --
| nan_to_na | Change nondetect representation |
| na_to_zero | Change nondetect representation |
| nfactors | stri_split and extract |
| normimpute | Impute from half-normal distribution around 0 |
-- O --
| occupancies | Get/Set occupancies |
| occupancies-method | Get/Set occupancies |
| occupancies<- | Get/Set occupancies |
| occupancies<--method | Get/Set occupancies |
-- P --
| pca | Add PCA, SMA, LDA, PLS |
| plot_biplot | Biplot |
| plot_boxplots | Plot sample/feature boxplots |
| plot_contrastogram | Plot contrastogram |
| plot_corrections | Biplot batch corrections |
| plot_covariates | Biplot covariates |
| plot_data | Plot data |
| plot_densities | Plot sample/feature densities |
| plot_detections | Plot detections |
| plot_detects | Plot detections |
| plot_features | Plot features |
| plot_feature_boxplots | Plot sample/feature boxplots |
| plot_feature_densities | Plot sample/feature densities |
| plot_feature_profiles | Plot features |
| plot_feature_violins | Plot sample/feature violins |
| plot_quantifications | Plot detections |
| plot_sample_boxplots | Plot sample/feature boxplots |
| plot_sample_densities | Plot sample/feature densities |
| plot_sample_violins | Plot sample/feature violins |
| plot_subgroup_boxplots | Plot sample/feature boxplots |
| plot_subgroup_violins | Plot sample/feature violins |
| plot_summarized_detections | Plot detections |
| plot_venn | Plot venn |
| plot_violins | Plot sample/feature violins |
| plot_volcano | Plot volcano |
| pls | Add PCA, SMA, LDA, PLS |
| preprocess_rnaseq_counts | Preprocess RNAseq counts |
| proteingroups | Get/Set proteingroups |
| proteingroups-method | Get/Set proteingroups |
| proteingroups<- | Get/Set proteingroups |
| proteingroups<--method | Get/Set proteingroups |
-- Q --
| quantnorm | Transform values |
-- R --
| read_affymetrix | Read affymetrix microarray |
| read_metabolon | Read metabolon |
| read_phosphosites | Read/Analyze proteingroups/phosphosites |
| read_proteingroups | Read/Analyze proteingroups/phosphosites |
| read_rectangles | Read omics data from rectangular file |
| read_rnaseq_bams | Read rnaseq |
| read_rnaseq_counts | Read rnaseq |
| read_somascan | Read somascan |
| rm_singleton_samples | Rm singleton samples |
-- S --
| sampleid_values | Get/Set svalues |
| scaledlibsizes | Get tmm-scaled libsizes |
| sdata | Get/Set sdata |
| sdata-method | Get/Set sdata |
| sdata<- | Get/Set sdata |
| sdata<--method | Get/Set sdata |
| slevels | Get slevels |
| sma | Add PCA, SMA, LDA, PLS |
| snames | Get/Set snames |
| snames-method | Get/Set snames |
| snames<- | Get/Set snames |
| snames<--method | Get/Set snames |
| split_by_svar | Split by svar |
| split_extract | stri_split and extract |
| standardize_maxquant_snames | Standardize maxquant snames |
| standardize_maxquant_snames.character | Standardize maxquant snames |
| standardize_maxquant_snames.SummarizedExperiment | Standardize maxquant snames |
| subgroup_array | Get subgroup matrix |
| subgroup_levels | Get slevels |
| subgroup_matrix | Get subgroup matrix |
| subgroup_values | Get/Set svalues |
| subtract_baseline | Subtract baseline |
| subtract_differences | Subtract baseline |
| subtract_pairs | Subtract baseline |
| sumexp2mae | Create MultiAssayExperiment from SummarizedExperiment list |
| sumexp_to_long_dt | Convert SummarizedExperiment into data.table |
| sumexp_to_subrep_dt | Convert SummarizedExperiment into data.table |
| sumexp_to_wide_dt | Convert SummarizedExperiment into data.table |
| summarize_fit | Summarize fit |
| svalues | Get/Set svalues |
| svalues<- | Get/Set svalues |
| svalues<--method | Get/Set svalues |
| svars | Get/Set svars |
| svars-method | Get/Set svars |
| svars<- | Get/Set svars |
| svars<--method | Get/Set svars |
-- T --
| TESTS | Statistical models supported in autonomics |
| tpm | Get/Set tpm |
| tpm-method | Get/Set tpm |
| tpm<- | Get/Set tpm |
| tpm<--method | Get/Set tpm |
| translate | Impute from half-normal distribution around 0 |
-- V --
| values | Get/Set expr values |
| values-method | Get/Set expr values |
| values<- | Get/Set expr values |
| values<--method | Get/Set expr values |
| venn_detects | Venn detects |
-- W --
| weights | Get/Set weights |
| weights-method | Get/Set weights |
| weights<- | Get/Set weights |
| weights<--method | Get/Set weights |
-- Z --
| zeroimpute | Impute from half-normal distribution around 0 |
| zero_to_na | Change nondetect representation |
| zscore | Transform values |
-- misc --
| .read_maxquant | Read/Analyze proteingroups/phosphosites |
| .read_metabolon | Read metabolon |
| .read_rectangles | Read omics data from rectangular file |
| .read_rnaseq_bams | Read rnaseq |
| .read_rnaseq_counts | Read rnaseq |
| .read_somascan | Read somascan |