Unified Statistical Modeling of Omics Data

Documentation for package ‘autonomics’ version 1.16.0

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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
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.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
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_compounddiscoverer_output	Is diann, fragpipe, proteingroups, phosphosites file?
assert_correlation_matrix	Assert correlation matrix
assert_diann_report	Is diann, fragpipe, proteingroups, phosphosites file?
assert_fastadt	Is fastadt
assert_fragpipe_tsv	Is diann, fragpipe, proteingroups, phosphosites file?
assert_is_fraction	Is fraction
assert_is_valid_sumexp	Assert that x is a valid SummarizedExperiment
assert_maxquant_phosphosites	Is diann, fragpipe, proteingroups, phosphosites file?
assert_maxquant_proteingroups	Is diann, fragpipe, proteingroups, phosphosites file?
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

-- B --

beta	Model based prediction
bin	Bin continuous variable
bin.character	Bin continuous variable
bin.factor	Bin continuous variable
bin.logical	Bin continuous variable
bin.numeric	Bin continuous variable
bin.SummarizedExperiment	Bin continuous variable
biplot	Biplot
biplot_corrections	Biplot batch corrections
biplot_covariates	Biplot covariates
block2lme	Put block in lme-compatible format
block2lme.character	Put block in lme-compatible format
block2lme.formula	Put block in lme-compatible format
block2lme.list	Put block in lme-compatible format
block_vars	Put block in lme-compatible format

-- C --

cbind_imputed	Split samples
center	Center samples
code	Contrast Code Factor
code.data.table	Contrast Code Factor
code.factor	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 coefs
coefs.data.table	Get coefs
coefs.factor	Get coefs
coefs.SummarizedExperiment	Get coefs
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
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
default_formula	Create default formula
default_geom	Default geom
default_sfile	Default sfile
default_subgroupvar	Create default formula
demultiplex	Demultiplex snames
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
exp2	Transform values
extract_coef_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 --

factor2logical	logical to factor
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	fitcoefs
fits	Get fit models
fits.data.table	Get fit models
fits.SummarizedExperiment	Get fit models
FITSEP	Fit results separator
fit_limma	Fit General Linear Model
fit_linmod	Fit General Linear Model
fit_lm	Fit General Linear Model
fit_lme	Fit General Linear Model
fit_lmer	Fit General Linear Model
fit_survival	Fit survival
fit_wilcoxon	Fit 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
formula2lm	Put block in lme-compatible format
formula2lmer	Put block in lme-compatible format
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
invert_subgroups	Invert subgroups
invnorm	Transform values
is_collapsed_subset	Is collapsed subset
is_compounddiscoverer_output	Is diann, fragpipe, proteingroups, phosphosites file?
is_correlation_matrix	Assert correlation matrix
is_diann_report	Is diann, fragpipe, proteingroups, phosphosites file?
is_fastadt	Is fastadt
is_file	Is a file?
is_fraction	Is fraction
is_fragpipe_tsv	Is diann, fragpipe, proteingroups, phosphosites 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 diann, fragpipe, proteingroups, phosphosites file?
is_maxquant_proteingroups	Is diann, fragpipe, proteingroups, phosphosites file?
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_connected_blocks	Keep fully connected blocks
keep_connected_features	Keep features with n+ connected blocks
keep_replicated_features	Keep replicated features

-- L --

label2index	Convert labels into indices
lda	PCA, SMA, LDA, PLS, SPLS, OPLS
LINMODENGINES	Linear Modeling Engines
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
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
modeldt	Get model variable
modeldt.data.table	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.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 --

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

-- 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_design	Plot model
plot_detections	Plot missingness per sample / subgroup
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_joint_density	Plot joint density
plot_matrix	Plot binary matrix
plot_sample_boxplots	Plot exprs for coef
plot_sample_densities	Plot sample/feature distributions
plot_sample_nas	Plot missingness per sample / subgroup
plot_sample_violins	Plot sample/feature violins
plot_subgroup_nas	Plot missingness per sample / subgroup
plot_subgroup_points	Plot features
plot_subgroup_violins	Plot sample/feature violins
plot_summarized_detections	Plot missingness per sample / subgroup
plot_summary	Plot summary
plot_survival	Plot survival
plot_venn	Plot venn
plot_venn_heatmap	Plot venn heatmap
plot_violins	Plot sample/feature violins
plot_volcano	Plot volcano
pls	PCA, SMA, LDA, PLS, SPLS, OPLS
pmat	Get model variable
PPATTERN	Fit results separator
PRECURSOR_QUANTITY	diann precursor quantity
preprocess_rnaseq_counts	Preprocess RNAseq counts
pull_columns	Pull columns in a dataframe to the front
pvar	Get model variable
pvec	Get model variable

-- Q --

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_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
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
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
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_longdt	SummarizedExperiment to data.table
sumexp_to_subrep_dt	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
SURVIVALENGINES	Survival engines
survival_example	Fit survival
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
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/ods
write_xl	Write xl/ods

-- X --

X	Model based prediction

-- Z --

zero_to_na	Change nondetect representation
zscore	Transform values

-- misc --

.coxph	Fit onefeature survival
.extract_effectsize_features	Extract coefficient features
.extract_fdr_features	Extract coefficient features
.extract_n_features	Extract coefficient features
.extract_p_features	Extract coefficient features
.extract_sign_features	Extract coefficient features
.fit_limma	Fit General Linear Model
.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