Package index

All functions

PCAdataplot()

Performs and plots the results of a PCA on omic data

RNAseqdata() print(<RNAseqdata>) plot(<RNAseqdata>)

Import, check and normalization and transformation of RNAseq data

Scenedesmus_metab Scenedesmus_apical

Concentration-response effect of triclosan in Scenedesmus vacuolatus

Zhou_kidney_pce

Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse

bmdboot() print(<bmdboot>) plot(<bmdboot>)

Computation of confidence interval on benchmark doses by bootstrap

bmdcalc() print(<bmdcalc>) plot(<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() print(<continuousanchoringdata>) plot(<continuousanchoringdata>)

Import and check of continuous anchoring apical data

curvesplot()

Plot of fitted curves

drcfit() print(<drcfit>) plot(<drcfit>) plotfit2pdf()

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() print(<itemselect>)

Selection of significantly responsive items

continuousomicdata() metabolomicdata() print(<continuousomicdata>) plot(<continuousomicdata>)

Import and check of continuous omic data (e.g. metabolomic data)

microarraydata() omicdata() print(<microarraydata>) plot(<microarraydata>)

Import, check and normalization of single-channel microarray data

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