Man pages for bhagwataditya/importomics
Unified statistal Modeling of Omics Data

abstract_fitAbstract model fit
add_adjusted_pvaluesAdd adjusted pvalues
add_assay_meansAdd assay means
add_facetvarsAdd facetvars
add_opentargets_by_uniprotAdd opentargets annotations
add_pspAdd psp
add_smilesAdd smiles
altenrichAlternative Enrichment Analysis
analysisGet/set analysis
analyzeAnalyze
annotate_maxquantAnnotate maxquant
annotate_uniprot_restAnnotate uniprot/ensp
assert_is_valid_sumexpAssert that x is a valid SummarizedExperiment
AUTONOMICS_DATASETSData used in examples/vignette/tests/longtests
binBin continuous variable
biplotBiplot
biplot_correctionsBiplot batch corrections
biplot_covariatesBiplot covariates
block2lmePut block in lme-compatible format
centerCenter samples
codeContrast Code Factor
coefsGet coefs
collapsed_entrezg_to_symbolCollapsed entrezg to genesymbol
COMPOUNDDISCOVERER_PATTERNScompound discoverer quantity patterns
CONTAMINANTSURLContaminants URL
contrast_subgroup_colsRow/Col contrasts
count_inCount/Collapse in/outside intersection
countsGet/Set counts
counts2cpmConvert between counts and cpm/tpm
counts2tpmcounts to tpm
cpmGet/Set cpm
create_designCreate design
default_coefsGet default coefs
default_formulaCreate default formula
default_geomDefault geom
default_sfileDefault sfile
demultiplexDemultiplex snames
dequantifyDequantify maxquant snames
dequantify_compounddiscovererdequantify_compounddiscoverer compound discoverer snames
dot-mergeClean Merge
dot-plot_survivalFit/Plot survival
dot-read_compounddiscovererRead compound discoverer files as-is
dot-read_maxquant_proteingroupsRead proteingroups/phosphosites as-is
download_contaminantsDownloads contaminants
download_dataDownload autonomics example data
download_gtfDownload GTF file
download_mcclain21Download mcclain21 data
download_tcga_exampleDownload tcga example
dt2mat'data.table' to 'matrix'
enrichmentEnrichment analysis
entrezg_to_symbolEntrezg to genesymbol
explore_transformationsExplore transformations
extract_coef_featuresExtract coefficient features
extract_rectangleExtract rectangle from omics file, data.table, or matrix
fclusterCluster features
fcorFeature correlations/distances
fdataGet/Set sample/feature data
fdr2pfdr to p
filter_exprs_replicated_in_some_subgroupFilter features with replicated expression in some subgroup
filter_featuresFilter features on condition
filter_medoidFilter medoid sample
filter_samplesFilter samples on condition
fitFit General Linear Model
fitcoefsfitcoefs
fit_lmxFit lm, lme, or lmer
fitsGet fit models
FITSEPFit results separator
fitvarsGet fit vars/dt
fix_xlgenesFix excel genes
flevelsGet fvar levels
fnamesGet/Set fnames
formula2strformula to string
fvaluesGet fvalues
fvarsGet/Set fvars
genome_to_orgdbGet corresponding orgdb
group_by_levelgroup by level
guess_compounddiscoverer_quantityGuess compound discoverer quantity from snames
guess_fitsepguess fitsep
guess_maxquant_quantityGuess maxquant quantity from snames
guess_sepGuess separator
has_multiple_levelsVariable has multiple levels?
hdlproteinshdl proteomewatch proteins
imputeImpute
invert_subgroupsInvert subgroups
is_collapsed_subsetIs collapsed subset
is_correlation_matrixAssert correlation matrix
is_diann_reportIs diann, fragpipe, proteingroups, phosphosites file?
is_fastadtIs fastadt
is_fileIs a file?
is_fractionIs fraction
is_imputedGet/set is_imputed
is_positive_numberIs positive number
is_scalar_subsetIs scalar subset
is_sigIs significant?
is_valid_formulaIs valid formula
keep_connected_blocksKeep fully connected blocks
keep_connected_featuresKeep features with n+ connected blocks
keep_replicated_featuresKeep replicated features
label2indexConvert labels into indices
LINMOD_ENGINESLinear Modeling Engines
list2matlist to matrix
list_fileslist files
log2countsGet/Set log2counts
log2cpmGet/Set log2cpm
log2diffsGet/Set log2diffs
log2proteinsGet/Set log2proteins
log2sitesGet/Set log2sites
log2tpmGet/Set log2tpm
log2transformTransform values
logical2factorlogical to factor
make_alpha_paletteMake alpha palette
make_colorsMake colors
make_volcano_dtCreate volcano datatable
map_fvaluesMap fvalues
matrix2sumexpConvert matrix into SummarizedExperiment
MAXQUANT_PATTERNSmaxquant quantity patterns
merge_compounddiscoverermerge compound discoverer files
merge_sample_excelMerge sample excel
merge_sample_fileMerge sample / feature file
merge_sdataMerge sample/feature dt
message_dfmessage dataframe
modelvarGet model variable
MSIGCOLLECTIONSHUMANHuman/Mouse Msigdb Collections
MSIGDIRlocal msigdb dir
OPENTARGETSDIRopentargets dir
order_on_pOrder on p
pcaPCA, SMA, LDA, PLS, SPLS, OPLS
percentilessurvival percentiles
pg_to_canonicalproteingroup to isoforms
plot_contrastogramPlot contrastogram
plot_contrast_vennPlot contrast venn
plot_dataPlot data
plot_densitiesPlot sample/feature distributions
plot_designPlot model
plot_exprsPlot exprs for coef
plot_exprs_per_coefPlot exprs per coef
plot_fit_summaryPlot fit summary
plot_heatmapPlot heatmap
plot_matrixPlot binary matrix
plot_model_summaryPlot model summary
plot_sample_nasPlot missingness per sample / subgroup
plot_subgroup_pointsPlot features
plot_summaryPlot summary
plot_vennPlot venn
plot_venn_heatmapPlot venn heatmap
plot_violinsPlot sample/feature violins
plot_volcanoPlot volcano
PRECURSOR_QUANTITYdiann precursor quantity
preprocess_rnaseq_countsPreprocess RNAseq counts
pull_columnsPull columns in a dataframe to the front
read_affymetrixRead affymetrix microarray
read_compounddiscovererRead maxquant proteingroups
read_contaminantsRead contaminants
read_diann_proteingroupsRead diann
read_fragpipeRead fragpipe
read_maxquant_phosphositesRead maxquant phosphosites
read_maxquant_proteingroupsRead maxquant proteingroups
read_metabolonRead metabolon xlsxfile
read_msigdtRead msigdb datatable
read_olinkRead olink file
read_rectanglesRead omics data from rectangular file
read_rnaseq_countsRead rnaseq counts/bams
read_salmonRead salmon
read_somascanRead somascan adatfile
read_uniprotdtRead fasta hdrs
reexportsObjects exported from other packages
reset_fitReset fit
rm_diann_contaminantsRm contaminants
rm_missing_in_some_samplesRm features missing in some samples
rm_unmatched_samplesrm unmatched/singleton samples
scaledlibsizesGet tmm-scaled libsizes
scorematExtract scores/loadings
slevelsGet slevels
snamesGet/Set snames
split_extract_fixedstri_split and extract
split_samplesSplit samples
stri_any_regexDoes any string have a regex
stri_detect_fixed_in_collapsedDetect fixed patterns in collapsed strings
subgroup_matrixGet subgroup matrix
subtract_baselineSubtract baseline
sumexplist_to_longdtSummarizedExperiment list to long data.table
sumexp_to_longdtSummarizedExperiment to data.table
sumexp_to_tsvWrite sumexp to tsv
summarize_fitSummarize fit
svaluesGet/Set svalues
svarsGet/Set svars
systematic_nasIs systematic/random/full NA
tag_featuresTag features
tag_hdlproteinsTag hdlproteins
taxon2orgtaxon/ens to organism
TAXON_TO_ORGNAMEAnnotation Maps
TESTSStatistical models supported in autonomics
tpmGet/Set tpm
twofactor_sumexptwofactor sumexp
uncollapseUncollapse/Recollapse
valuesGet/Set expr values
varlevels_dont_clashAre varlevels unique
venn_detectsVenn detects
weightsGet/Set weights
write_xlWrite xl/ods
zero_to_naChange nondetect representation
bhagwataditya/importomics documentation built on June 15, 2024, 1:05 a.m.