Unified statistal Modeling of Omics Data


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Documentation for package ‘autonomics’ version 1.12.0

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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 Z misc

-- A --

ABBREV_TO_ORGNAME Annotation Maps
abstractvar Get model variable
abstract_fit Abstract model fit
add_adjusted_pvalues 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_maxquant Annotate maxquant
annotate_uniprot_rest Annotate uniprot/ensp
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 --

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
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
CONTAMINANTSURL Contaminants URL
contr.diff Contrast Code Factor
contr.treatment.explicit Contrast Code Factor
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
create_design.data.table Create design
create_design.SummarizedExperiment Create design

-- 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
downfeatures Get model variable
download_contaminants Downloads contaminants
download_data Download autonomics example data
download_gtf Download GTF file
download_mcclain21 Download mcclain21 data
download_tcga_example Download tcga example
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
explore_transformations Explore transformations
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
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
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
fit Fit model and test for differential expression
fitcoefs fitcoefs
fitdt Get fit vars/dt
fits Get fit models
FITSEP Fit results separator
fitvars Get fit vars/dt
fit_limma Fit model and test for differential expression
fit_lm Fit lm, lme, or lmer
fit_lme Fit lm, lme, or lmer
fit_lmer Fit lm, lme, or lmer
fit_lmx Fit lm, lme, or lmer
fit_survival Fit/Plot survival
fit_wilcoxon Fit model and test for differential expression
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
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_fitsep 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_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
LINMOD_ENGINES 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
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
modelfeatures Get model variable
modelmat Get model variable
modelvar Get model variable
modelvec Get model variable
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

-- P --

parse_maxquant_hdrs Read fasta hdrs
pca PCA, SMA, LDA, PLS, SPLS, OPLS
pdt Get model variable
percentiles survival percentiles
pg_to_canonical proteingroup to isoforms
pg_to_isoforms proteingroup to isoforms
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_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 Fit/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_contaminantdt Read fasta hdrs
read_contaminants Read contaminants
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
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
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
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
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

-- 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

-- Z --

zero_to_na Change nondetect representation
zscore Transform values

-- misc --

.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 model and test for differential expression
.merge Clean Merge
.plot_survival Fit/Plot survival
.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