Dose Response for Omics

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Documentation for package ‘DRomics’ version 2.5-2

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

Help Pages

bmdboot	Computation of confidence interval on benchmark doses by bootstrap
bmdcalc	Computation of benchmark doses for responsive items
bmdfilter	Filtering BMDs according to estimation quality
bmdplot	BMD plot optionally with confidence intervals on BMD
bmdplotwithgradient	BMD plot with color gradient
continuousanchoringdata	Import and check of continuous anchoring apical data
continuousomicdata	Import and check of continuous omic data (e.g. metabolomic data)
curvesplot	Plot of fitted curves
drcfit	Dose response modelling for responsive items
ecdfplotwithCI	ECDF plot of a variable with given confidence intervals on this variable
ecdfquantileplot	ECDF plot of a given quantile of a variable calculated by group
formatdata4DRomics	Build an R object that can be used as data input in DRomics
itemselect	Selection of significantly responsive items
metabolomicdata	Import and check of continuous omic data (e.g. metabolomic data)
microarraydata	Import, check and normalization of single-channel microarray data
omicdata	Import, check and normalization of single-channel microarray data
PCAdataplot	Performs and plots the results of a PCA on omic data
plot.bmdboot	Computation of confidence interval on benchmark doses by bootstrap
plot.bmdcalc	Computation of benchmark doses for responsive items
plot.continuousanchoringdata	Import and check of continuous anchoring apical data
plot.continuousomicdata	Import and check of continuous omic data (e.g. metabolomic data)
plot.drcfit	Dose response modelling for responsive items
plot.microarraydata	Import, check and normalization of single-channel microarray data
plot.RNAseqdata	Import, check and normalization and transformation of RNAseq data
plotfit2pdf	Dose response modelling for responsive items
print.bmdboot	Computation of confidence interval on benchmark doses by bootstrap
print.bmdcalc	Computation of benchmark doses for responsive items
print.continuousanchoringdata	Import and check of continuous anchoring apical data
print.continuousomicdata	Import and check of continuous omic data (e.g. metabolomic data)
print.drcfit	Dose response modelling for responsive items
print.itemselect	Selection of significantly responsive items
print.microarraydata	Import, check and normalization of single-channel microarray data
print.RNAseqdata	Import, check and normalization and transformation of RNAseq data
RNAseqdata	Import, check and normalization and transformation of RNAseq data
Scenedesmus	Concentration-response effect of triclosan in Scenedesmus vacuolatus
Scenedesmus_apical	Concentration-response effect of triclosan in Scenedesmus vacuolatus
Scenedesmus_metab	Concentration-response effect of triclosan in Scenedesmus vacuolatus
selectgroups	Selection of groups on which to focus
sensitivityplot	Plot of a summary of BMD values per group of items
targetplot	Dose-reponse plot for target items
trendplot	Plot of the repartition of trends per group
zebraf	Transcriptomic dose-response to ionizing radiation in zebrafish with batch effect
Zhou	Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse
Zhou_kidney_pce	Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse