# Generifying and intuifying cross-platform omics analysis

## Documentation for package ‘autonomics’ version 1.4.0

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

## 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