R: Unified Statistical Modeling of Omics Data

# Unified Statistical Modeling of Omics Data

## Documentation for package ‘autonomics’ version 1.20.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W X Z misc

## -- A --

ABBREV_TO_ORGNAME | Annotation Maps
abind | Sample/Feature/Assay bind
abstractvar | Get model variable
abstractvar.data.table | Get model variable
abstractvar.SummarizedExperiment | Get model variable
abstractvec | Get model variable
abstractvec.data.table | Get model variable
abstractvec.SummarizedExperiment | Get model variable
abstract_fit | Abstract model fit
add_adjusted_pvalues | Add adjusted pvalues
add_adjusted_pvalues.data.table | Add adjusted pvalues
add_adjusted_pvalues.NULL | Add adjusted pvalues
add_adjusted_pvalues.SummarizedExperiment | Add adjusted pvalues
add_assay_means | Add assay means
add_facetvars | Add facetvars
add_opentargets_by_uniprot | Add opentargets annotations
add_psp | Add psp
add_smiles | Add smiles
all_non_numeric | Are all variables non-numeric ?
altenrich | Alternative Enrichment Analysis
analysis | Get/set analysis
analysis-method | Get/set analysis
analysis<- | Get/set analysis
analysis<--method | Get/set analysis
analyze | Analyze
annotate_compounddiscoverer | Read compound discoverer output
annotate_maxquant | Annotate maxquant
annotate_uniprot_rest | Annotate uniprot/ensp
assert_character_matrix | Is character matrix
assert_compounddiscoverer_output | Is diann report ?
assert_correlation_matrix | Assert correlation matrix
assert_diann_report | Is diann report ?
assert_fastadt | Is fastadt
assert_fragpipe_tsv | Is diann report ?
assert_is_fraction | Is fraction
assert_is_valid_sumexp | Assert that x is a valid SummarizedExperiment
assert_maxquant_phosphosites | Is diann report ?
assert_maxquant_proteingroups | Is diann report ?
assert_positive_number | Is positive number
assert_scalar_subset | Is scalar subset
assert_valid_formula | Is valid formula
assert_weakly_positive_number | Is positive number
AUTONOMICS_DATASETS | Data used in examples/vignette/tests/longtests
awblinmod | General Linear Modeling (across-within-between interface)
awblinmod_limma | General Linear Modeling (across-within-between interface)
awblinmod_lm | General Linear Modeling (across-within-between interface)
awblinmod_lme | General Linear Modeling (across-within-between interface)
awblinmod_lmer | General Linear Modeling (across-within-between interface)

## -- B --

beta | Model based prediction
bin | Factorize/Bin
bin.character | Factorize/Bin
bin.factor | Factorize/Bin
bin.logical | Factorize/Bin
bin.matrix | Factorize/Bin
bin.numeric | Factorize/Bin
bin.SummarizedExperiment | Factorize/Bin
bin_assay | Factorize/Bin
biplot | Biplot
biplot_corrections | Biplot batch corrections
biplot_covariates | Biplot covariates
biplot_transforms | Visually evaluate transformation effects
biplot_transforms_assays | Visually evaluate transformation effects
block2limma | block2limma
block2limma.character | block2limma
block2limma.formula | block2limma
block2limma.list | block2limma
block2limma.NULL | block2limma
block2lm | block2lm
block2lm.character | block2lm
block2lm.formula | block2lm
block2lm.list | block2lm
block2lm.NULL | block2lm
block2lme | block2lme
block2lme.character | block2lme
block2lme.formula | block2lme
block2lme.list | block2lme
block2lmer | block2lmer
block2lmer.character | block2lmer
block2lmer.formula | block2lmer
block2lmer.list | block2lmer
block_has_two_levels | Block has two levels

## -- C --

cbind_imputed | Split samples
center | Center samples
center_mean | Center samples
center_median | Center samples
code | Contrast Code Factor
code.character | Contrast Code Factor
code.data.table | Contrast Code Factor
code.factor | Contrast Code Factor
code.logical | Contrast Code Factor
code.numeric | Contrast Code Factor
code_control | Contrast Code Factor
code_deviation | Contrast Code Factor
code_deviation_first | Contrast Code Factor
code_diff | Contrast Code Factor
code_diff_forward | Contrast Code Factor
code_helmert | Contrast Code Factor
code_helmert_forward | Contrast Code Factor
coefs | Get fit models
coefs.data.table | Get fit models
coefs.factor | Get fit models
coefs.NULL | Get fit models
coefs.SummarizedExperiment | Get fit models
coefs_estimable | Are coefs/pvalues estimable
collapsed_entrezg_to_symbol | Collapsed entrezg to genesymbol
collapse_in | Count/Collapse in/outside intersection
collapse_in.character | Count/Collapse in/outside intersection
collapse_in.factor | Count/Collapse in/outside intersection
collapse_in.list | Count/Collapse in/outside intersection
COMPOUNDDISCOVERER_PATTERNS | compound discoverer quantity patterns
contr.diff | Contrast Code Factor
contr.treatment.explicit | Contrast Code Factor
contrastdt | Get contrastdt
contrast_coefs | Get model coefs
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/tpm
counts2tpm | counts to tpm
counts<- | Get/Set counts
counts<--method | Get/Set counts
count_in | Count/Collapse in/outside intersection
count_in.character | Count/Collapse in/outside intersection
count_in.factor | Count/Collapse in/outside intersection
count_in.list | Count/Collapse in/outside intersection
count_out | Count/Collapse in/outside intersection
count_out.character | Count/Collapse in/outside intersection
count_out.factor | Count/Collapse in/outside intersection
count_out.list | Count/Collapse in/outside intersection
cpm | Get/Set cpm
cpm-method | Get/Set cpm
cpm2counts | Convert between counts and cpm/tpm
cpm<- | Get/Set cpm
cpm<--method | Get/Set cpm
create_design | Create design matrix
create_design.data.table | Create design matrix
create_design.SummarizedExperiment | Create design matrix

## -- D --

DATADIR | Download autonomics example data
defaultmsigfile | Default msigdb file
default_formula | Create default formula
default_geom | Default geom
default_sfile | Default sfile
demultiplex | Demultiplex snames
densities | Densities
dequantify | Dequantify maxquant snames
dequantify_compounddiscoverer | dequantify_compounddiscoverer compound discoverer snames
DIMREDENGINES | Dimension Reduction Methods
DIMREDSUPER | Dimension Reduction Methods
DIMREDUN | Dimension Reduction Methods
downfeatures | Get model variable
download_data | Download autonomics example data
download_gtf | Download GTF file
download_mcclain21 | Download mcclain21 data
dt2mat | 'data.table' to 'matrix'

## -- E --

effectdt | Get model variable
effectmat | Get model variable
effectsizemat | Get model variable
effectvar | Get model variable
effectvec | Get model variable
enrichment | Enrichment analysis
ens2org | taxon/ens to organism
entrezg_to_symbol | Entrezg to genesymbol
EXISTENCE_TO_NUMBER | Annotation Maps
exp2transform | Transform values
extract_contrast_features | Extract coefficient 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 --

factor.vars | Get factor variables
factor.vars-method | Get factor variables
factor2logical | logical to factor
factorize | Factorize/Bin
factorize.character | Factorize/Bin
factorize.factor | Factorize/Bin
factorize.logical | Factorize/Bin
factorize.matrix | Factorize/Bin
factorize.numeric | Factorize/Bin
factorize.SummarizedExperiment | Factorize/Bin
factorize_assay | Factorize/Bin
fbind | Sample/Feature/Assay bind
fcluster | Cluster features
fcor | Feature correlations/distances
fdata | Get/Set sample/feature data
fdata-method | Get/Set sample/feature data
fdata<- | Get/Set sample/feature data
fdata<--method | Get/Set sample/feature data
fdist | Feature correlations/distances
fdr2p | fdr to p
fdrmat | Get model variable
fdrvar | Get model variable
fdrvec | Get model variable
fdt | Get/Set sample/feature data
fdt-method | Get/Set sample/feature data
fdt<- | Get/Set sample/feature data
fdt<--method | Get/Set sample/feature data
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_samples | Filter samples on condition
fitcoefs | Get fit models
fits | Get fit models
fits.data.table | Get fit models
fits.NULL | Get fit models
fits.SummarizedExperiment | Get fit models
fit_limma | General Linear Model
fit_lm | General Linear Model
fit_lme | General Linear Model
fit_lmer | General Linear Model
fit_survival | Fit/Plot survival
fit_wilcoxon | General Linear Model
fix_xlgenes | Fix excel genes
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
fscale | Transform values
ftype | Feature type
fvalues | Get fvalues
fvars | Get/Set fvars
fvars-method | Get/Set fvars
fvars<- | Get/Set fvars
fvars<--method | Get/Set fvars

## -- G --

genome_to_orgdb | Get corresponding orgdb
group_by_level | group by level
group_by_level.character | group by level
group_by_level.data.table | group by level
group_by_level.factor | group by level
guess_compounddiscoverer_quantity | Guess compound discoverer quantity from snames
guess_fitsep | guess fitsep
guess_fitsep.data.table | guess fitsep
guess_fitsep.SummarizedExperiment | guess fitsep
guess_maxquant_quantity | Guess maxquant quantity from snames
guess_sep | Guess separator
guess_sep.character | Guess separator
guess_sep.factor | Guess separator
guess_sep.numeric | Guess separator
guess_sep.SummarizedExperiment | Guess separator

## -- H --

has_multiple_levels | Variable has multiple levels?
has_multiple_levels.character | Variable has multiple levels?
has_multiple_levels.data.table | Variable has multiple levels?
has_multiple_levels.factor | Variable has multiple levels?
has_multiple_levels.numeric | Variable has multiple levels?
has_multiple_levels.SummarizedExperiment | Variable has multiple levels?
hdlproteins | hdl proteomewatch proteins

## -- I --

impute | Impute
impute.matrix | Impute
impute.numeric | Impute
impute.SummarizedExperiment | Impute
inf_to_na | Change nondetect representation
installed | Is package installed?
invert_subgroups | Invert subgroups
invnorm | Transform values
is_character_matrix | Is character matrix
is_collapsed_subset | Is collapsed subset
is_compounddiscoverer_output | Is compounddiscoverer output?
is_correlation_matrix | Assert correlation matrix
is_diann_report | Is diann report ?
is_fastadt | Is fastadt
is_file | Is a file?
is_fraction | Is fraction
is_fragpipe_tsv | Is fragpipe file?
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_maxquant_phosphosites | Is maxquant phosphosites file?
is_maxquant_proteingroups | Is maxquant proteingroups file?
is_non_numeric | Are all variables non-numeric ?
is_positive_number | Is positive number
is_scalar_subset | Is scalar subset
is_sig | Is significant?
is_valid_formula | Is valid formula
is_weakly_positive_number | Is positive number

## -- K --

keep_estimable_features | Keep estimable features

## -- L --

label2index | Convert labels into indices
lda | PCA, SMA, LDA, PLS, SPLS, OPLS
left.vars | Get factor variables
LINMOD | General Linear Model
LINMODENGINES | Linear Modeling Engines
linmod_limma | General Linear Model
linmod_lm | General Linear Model
linmod_lme | General Linear Model
linmod_lmer | General Linear Model
linmod_wilcoxon | General Linear Model
list2mat | list to matrix
list_files | list files
loadingmat | Extract scores/loadings
loadings | Extract scores/loadings
log2counts | Get/Set log2counts
log2counts-method | Get/Set log2counts
log2counts<- | Get/Set log2counts
log2counts<--method | Get/Set log2counts
log2cpm | Get/Set log2cpm
log2cpm-method | Get/Set log2cpm
log2cpm<- | Get/Set log2cpm
log2cpm<--method | Get/Set log2cpm
log2diffs | Get/Set log2diffs
log2diffs-method | Get/Set log2diffs
log2diffs<- | Get/Set log2diffs
log2diffs<--method | Get/Set log2diffs
log2proteins | Get/Set log2proteins
log2proteins-method | Get/Set log2proteins
log2proteins<- | Get/Set log2proteins
log2proteins<--method | Get/Set log2proteins
log2sites | Get/Set log2sites
log2sites-method | Get/Set log2sites
log2sites<- | Get/Set log2sites
log2sites<--method | Get/Set log2sites
log2tpm | Get/Set log2tpm
log2tpm-method | Get/Set log2tpm
log2tpm<- | Get/Set log2tpm
log2tpm<--method | Get/Set log2tpm
log2transform | Transform values
logical2factor | logical to factor

## -- M --

make_alpha_palette | Make alpha palette
make_colors | Make colors
make_volcano_dt | Create volcano datatable
map_fvalues | Map fvalues
mat2dt | 'data.table' to 'matrix'
matrix2sumexp | Convert matrix into SummarizedExperiment
MAXQUANT_PATTERNS | maxquant quantity patterns
mclust_breaks | Mixture/Quantile breaks
mclust_parameters | Distribution parameters
mdsplot | Feature correlations/distances
merge_compounddiscoverer | merge compound discoverer files
merge_fdata | Merge sample/feature dt
merge_fdt | Merge sample/feature dt
merge_ffile | Merge sample / feature file
merge_sample_excel | Merge sample excel
merge_sample_file | Merge sample / feature file
merge_sdata | Merge sample/feature dt
merge_sdt | Merge sample/feature dt
message_df | message dataframe
minusinf_to_na | Change nondetect representation
mixtools_breaks | Mixture/Quantile breaks
mixtools_parameters | Distribution parameters
modeldt | Get model variable
modeldt.data.table | Get model variable
modeldt.NULL | Get model variable
modeldt.SummarizedExperiment | Get model variable
modelfeatures | Get model variable
modelfeatures.data.table | Get model variable
modelfeatures.SummarizedExperiment | Get model variable
modelmat | Get model variable
modelvar | Get model variable
modelvar.data.table | Get model variable
modelvar.NULL | Get model variable
modelvar.SummarizedExperiment | Get model variable
modelvec | Get model variable
modelvec.data.table | Get model variable
modelvec.SummarizedExperiment | Get model variable
model_coefs | Get model coefs
MSIGCOLLECTIONSHUMAN | Human/Mouse Msigdb Collections
MSIGCOLLECTIONSMOUSE | Human/Mouse Msigdb Collections
MSIGDIR | local msigdb dir

## -- N --

nan_to_na | Change nondetect representation
na_to_string | Change nondetect representation
na_to_zero | Change nondetect representation
nfactors | stri_split and extract
no_nas | Is systematic/random/full NA

## -- O --

object1 | Example objects for binding
object2 | Example objects for binding
OPENTARGETSDIR | opentargets dir
opls | PCA, SMA, LDA, PLS, SPLS, OPLS
order_on_effect | Order on p
order_on_p | Order on p
order_on_t | Order on p
overall_parameters | Distribution parameters

## -- P --

parse_maxquant_hdrs | Read fasta hdrs
pca | PCA, SMA, LDA, PLS, SPLS, OPLS
pdt | Get model variable
pg_to_canonical | proteingroup to isoforms
pg_to_isoforms | proteingroup to isoforms
plot_coef_densities | Plot contrast densities
plot_contrastogram | Plot contrastogram
plot_contrast_venn | Plot contrast venn
plot_data | Plot data
plot_densities | Plot sample/feature distributions
plot_densities_transforms | Visually evaluate transformation effects
plot_design | Plot model
plot_detections | Plot (summarized) detections
plot_exprs | Plot exprs for coef
plot_exprs_per_coef | Plot exprs per coef
plot_feature_boxplots | Plot exprs for coef
plot_feature_densities | Plot sample/feature distributions
plot_feature_violins | Plot sample/feature violins
plot_fit_summary | Plot fit summary
plot_heatmap | Plot heatmap
plot_matrix | Plot binary matrix
plot_sample_boxplots | Plot exprs for coef
plot_sample_densities | Plot sample/feature distributions
plot_sample_nas | Plot (summarized) detections
plot_sample_violins | Plot sample/feature violins
plot_subgroup_nas | Plot (summarized) detections
plot_subgroup_points | Plot features
plot_subgroup_violins | Plot sample/feature violins
plot_summarized_detections | Plot (summarized) detections
plot_summary | Plot summary
plot_survival | Fit/Plot survival
plot_venn | Plot venn
plot_venn_heatmap | Plot venn heatmap
plot_violins | Plot sample/feature violins
plot_violins_transforms | Visually evaluate transformation effects
plot_volcano | Plot volcano
plot_xy_density | Plot xy densities
plot_xy_scatter | Plot xy densities
plot_x_density | Plot xy densities
plot_y_density | Plot xy densities
pls | PCA, SMA, LDA, PLS, SPLS, OPLS
pmat | Get model variable
PRECURSOR_QUANTITY | diann precursor quantity
preprocess_rnaseq_counts | Preprocess RNAseq counts
prep_survival | Fit/Plot survival
pull_columns | Pull columns in a dataframe to the front
pvalues_estimable | Are coefs/pvalues estimable
pvar | Get model variable
pvec | Get model variable

## -- Q --

quantile_breaks | Mixture/Quantile breaks
quantnorm | Transform values

## -- R --

random_nas | Is systematic/random/full NA
read_affymetrix | Read affymetrix microarray
read_compounddiscoverer | Read compound discoverer output
read_contaminantdt | Read fasta hdrs
read_diann | Read diann
read_diann_pgmatrix | Read diann phosphosites
read_diann_phosphodiffs | Read diann phosphosites
read_diann_phosphosites | Read diann phosphosites
read_diann_proteingroups | Read diann
read_fragpipe | Read fragpipe
read_maxquant_phosphosites | Read maxquant phosphosites
read_maxquant_proteingroups | Read maxquant proteingroups
read_metabolon | Read metabolon xlsxfile
read_msigdt | Read msigdb datatable
read_olink | Read olink file
read_phosphosites | Read maxquant phosphosites
read_proteingroups | Read maxquant proteingroups
read_rectangles | Read omics data from rectangular file
read_rnaseq_bams | Read rnaseq counts/bams
read_rnaseq_counts | Read rnaseq counts/bams
read_salmon | Read salmon
read_somascan | Read somascan adatfile
read_uniprotdt | Read fasta hdrs
recollapse | Uncollapse/Recollapse
reset_fit | Reset fit
REVIEWED_TO_NUMBER | Annotation Maps
right.vars | Get factor variables
rm_diann_contaminants | Rm contaminants
rm_missing_in_all_samples | Rm features missing in some samples
rm_missing_in_some_samples | Rm features missing in some samples
rm_singleton_samples | rm unmatched/singleton samples
rm_unmatched_samples | rm unmatched/singleton samples

## -- S --

sampleid_values | Get/Set svalues
sbind | Sample/Feature/Assay bind
scaledlibsizes | Get tmm-scaled libsizes
scor | Feature correlations/distances
scoremat | Extract scores/loadings
scores | Extract scores/loadings
sdata | Get/Set sample/feature data
sdata-method | Get/Set sample/feature data
sdata<- | Get/Set sample/feature data
sdata<--method | Get/Set sample/feature data
sdist | Feature correlations/distances
sdt | Get/Set sample/feature data
sdt-method | Get/Set sample/feature data
sdt<- | Get/Set sample/feature data
sdt<--method | Get/Set sample/feature data
slevels | Get slevels
sma | PCA, SMA, LDA, PLS, SPLS, OPLS
snames | Get/Set snames
snames-method | Get/Set snames
snames<- | Get/Set snames
snames<--method | Get/Set snames
split_extract | stri_split and extract
split_extract_fixed | stri_split and extract
split_extract_regex | stri_split and extract
split_features | Split samples
split_samples | Split samples
spls | PCA, SMA, LDA, PLS, SPLS, OPLS
sscale | Transform values
stepauc | Compute step auc
stri_any_regex | Does any string have a regex
stri_detect_fixed_in_collapsed | Detect fixed patterns in collapsed strings
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
sumexplist_to_longdt | SummarizedExperiment list to long data.table
sumexp_to_groupdt | SummarizedExperiment to data.table
sumexp_to_longdt | SummarizedExperiment to data.table
sumexp_to_tsv | Write sumexp to tsv
sumexp_to_widedt | SummarizedExperiment to data.table
summarize_fit | Summarize fit
summarize_fit.data.table | Summarize fit
summarize_fit.SummarizedExperiment | Summarize fit
survobj | Survival analysis example
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
systematic_nas | Is systematic/random/full NA

## -- T --

tag_features | Tag features
tag_hdlproteins | Tag hdlproteins
taxon2org | taxon/ens to organism
TAXON_TO_ORGNAME | Annotation Maps
tdt | Get model variable
TESTS | Statistical models supported in autonomics
tmat | Get model variable
tpm | Get/Set tpm
tpm-method | Get/Set tpm
tpm<- | Get/Set tpm
tpm<--method | Get/Set tpm
TRANSFORMENGINES | Data Transformation Methods
TRANSFORMSTRICT | Data Transformation Methods
tvar | Get model variable
tvec | Get model variable
twofactor_sumexp | twofactor sumexp

## -- U --

uncollapse | Uncollapse/Recollapse
upfeatures | Get model variable

## -- V --

values | Get/Set expr values
values-method | Get/Set expr values
values<- | Get/Set expr values
values<--method | Get/Set expr values
varlevels_dont_clash | Are varlevels unique
varlevels_dont_clash.data.table | Are varlevels unique
varlevels_dont_clash.SummarizedExperiment | Are varlevels unique
venn_detects | Venn detects
vsn | Transform values

## -- W --

weights | Get/Set weights
weights-method | Get/Set weights
weights<- | Get/Set weights
weights<--method | Get/Set weights
write_ods | Write xl
write_xl | Write xl

## -- X --

X | Model based prediction

## -- Z --

zero_to_na | Change nondetect representation
zscore | Transform values

## -- misc --

.coxph | Fit onefeature survival
.densities | Densities
.extract_effectsize_features | Extract coefficient features
.extract_fdr_features | Extract coefficient features
.extract_n_features | Extract coefficient features
.extract_p_features | Extract coefficient features
.fit_survival | Fit/Plot survival
.logrank | Fit onefeature survival
.merge | Clean Merge
.read_compounddiscoverer | Read compound discoverer files as-is
.read_compounddiscoverer_masslist | Read compound discoverer masslist files as-is
.read_diann_precursors | Read diann
.read_diann_proteingroups | Read diann
.read_maxquant_phosphosites | Read proteingroups/phosphosites as-is
.read_maxquant_proteingroups | Read proteingroups/phosphosites as-is
.read_metabolon | Read metabolon xlsxfile
.read_rectangles | Read omics data from rectangular file
.read_rnaseq_bams | Read rnaseq counts/bams
.read_rnaseq_counts | Read rnaseq counts/bams
.read_somascan | Read somascan adatfile
.survdiff | Fit onefeature survival