Package: SARP.compo 0.1.8

SARP.compo: Network-Based Interpretation of Changes in Compositional Data

Provides a set of functions to interpret changes in compositional data based on a network representation of all pairwise ratio comparisons: computation of all pairwise ratio, construction of a p-value matrix of all pairwise tests of these ratios between conditions, conversion of this matrix to a network.

Authors:Emmanuel Curis [aut, cre]

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SARP.compo.pdf |SARP.compo.html✨
SARP.compo/json (API)

# Install 'SARP.compo' in R:
install.packages('SARP.compo', repos = c('https://ecuris.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • BpLi_J2 - Circadian Genes Expression in Bipolar Disorder Patients
  • BpLi_J4 - Circadian Genes Expression in Bipolar Disorder Patients
  • GADL1 - Gene expression change in bipolar disorder
  • SCH23390 - Effect of MDMA and SCH23390 on gene expression
  • generef - Expression level of candidate reference genes
  • poteries - Composition of Roman poteries

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

23 exports 0.09 score 60 dependencies 22 scripts 248 downloads

Last updated 7 months agofrom:9fdb795439. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-winOKSep 02 2024
R-4.5-linuxOKSep 02 2024
R-4.4-winOKSep 02 2024
R-4.4-macOKSep 02 2024
R-4.3-winOKSep 02 2024
R-4.3-macOKSep 02 2024

Exports:anva_SC.fpcanva1.fpcanva1vi.fpcarbre.Mpcalc.rapportschoisir.seuilchoisir.seuil.equivcoupures.Mpcreer.DFpcreer.Fpcreer.Mpdistrib.distancesequiv.fpcestimer.alphaestimer.puissancegrf.DFpgrf.Fpgrf.Mpkw.fpcmodele_compoMp.DFprls.fpcstudent.fpc

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecowplotcpp11DerivdoBydplyrfansifarvergenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrquantregR6RColorBrewerRcppRcppEigenrlangscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Grouping composants by changes in cut-off separationarbre.Mp plot.Arbre
Circadian Genes Expression in Bipolar Disorder PatientsBpLi_J2 BpLi_J4
Compute all pairwise ratios of a set of variablescalc.rapports
Cut-off selection by simulationschoisir.seuil plot.SARPcompo.H0 print.SARPcompo.H0
Cut-off selection by simulations, in the context of equivalence testschoisir.seuil.equiv
Convert between matrix and data-frame formatconversions DFp.Mp Mp.DFp
Finding cut-offs for graph disjonctionscoupures.Mp plot.Coupures
Create p-values data-frame from pairwise tests of all possible ratios of a compositional vectorcreate.DFp creer.DFp creer_data.frame
Create a graph using a set of p-values from pairwise testscreate.graphe creer_graphe grf.DFp grf.Mp
Create p-values matrix from pairwise tests of all possible ratios of a compositional vectorcreate.Mp creer.Mp creer_matrice
Simulate the distribution of maximal minimal distances in a random graphdistrib.distances
Utility function to obtain p-value for equivalence tests on individual ratiosequiv.fpc equivalence
Create and read a file of p-values for all pairwise tests of all possible ratios of a compositional vectorcreate.Fp creer.Fp fichier grf.Fp
Gene expression change in bipolar disorderGADL1 gadl1
Expression level of candidate reference genesCq.reference generef
Create a compositional model for simulationsmodele modele_compo plot.SARPcompo.modele
Composition of Roman poteriespoteries
Estimate the power and the type-I error of the disjoint-subgraphs methodalpha estimer.alpha estimer.puissance puissance
Effect of MDMA and SCH23390 on gene expressionSCH23390 sch23390
Utility functions to obtain p-values from tests on individual ratiosanva1.fpc anva1vi.fpc anva_SC.fpc kw.fpc rls.fpc student.fpc tests