Files in genostats/FEstim
Genetic Data Analyses in Presence of Inbreeding
.gitignore
DESCRIPTION
NAMESPACE
Poster/Poster_IGES_2022.pdf
QUESTIONS
R/Fantasio.r
R/HBDOverlap.r
R/HBDPlotChr.r
R/HBDPlotId.r
R/HBDSegments.r
R/HBDSegmentsBySegments.r
R/HBDSegmentsBySnps.r
R/HFLODManhattanPlot.r
R/HFLODPlotChr.r
R/RcppExports.R
R/addCM.r
R/atlas.r
R/bedLogEmiss.r
R/cleanHotspots.r
R/color.r
R/data.r
R/fMatrix.r
R/festim.r
R/forwardBackward.r
R/getIdOverlap.r
R/getLogEmiss.r
R/getMarkerChromosomByDistance.r
R/getPosition.r
R/ggQQPlot.r
R/glmHBD.r
R/glmHBDPlot.r
R/hotspotsMatrix.r
R/hotspotsSegments.r
R/importExport.r
R/lengthChromosome.r
R/likelihood.r
R/likelihoodGradient.r
R/logProbaEmission.r
R/makeAtlasByDistance.r
R/makeAtlasByHotspots.r
R/makeSubmapByDistance.r
R/makeSubmapByHotspots.r
R/markerRepresentation.r
R/markerSummary.r
R/msatMatrix.r
R/nullRemover.r
R/paintCytobands.r
R/phenoConverter.r
R/plotHBDSegmentsChr.r
R/plotHBDSegmentsId.r
R/plotROHSegmentsChr.r
R/plotROHSegmentsId.r
R/plotSegmentsChr.r
R/plotSegmentsId.r
R/readMsatMatrix.r
R/recap.r
R/recapBySegments.r
R/recapBySnps.r
R/segmentsListByDistance.r
R/segmentsListByHotspots.r
R/segmentsListSummary.r
R/selectMarkerDownstream.r
R/selectMarkerUpstream.r
R/setAlleleFrequencies.r
R/setFLOD.r
R/setHBDProb.r
R/setHBDProbAndFLOD.r
R/setHBDProbAndFLODBySnps.r
R/setHFLOD.r
R/setStatus.r
R/setSummary.r
R/simus.r
R/snpsMatrix.r
R/snpsSegments.r
R/submapEstim.r
R/submapFLODRecap.r
R/submapHBDRecap.r
R/submapLikelihood.r
R/submapSummary.r
R/uniqueIds.r
R/unitPlotChr.r
R/unitPlotId.r
TODO
data/cytobands.b35.rda
data/cytobands.b36.rda
data/cytobands.b37.rda
data/cytobands.b38.rda
data/datalist
data/hotspot_hg17.rda
data/hotspot_hg18.rda
data/hotspot_hg19.rda
inst/extdata/data_msat.in
inst/extdata/data_snp.in
inst/extdata/in_datall.txt
inst/extdata/in_markall.txt
inst/extdata/map_msat.in
inst/extdata/map_snp.in
inst/include/Fantasio.h
man/Fantasio.Rd
man/HBDPlotChr.Rd
man/HBDPlotId.Rd
man/HBDSegments.Rd
man/HFLODManhattanPlot.Rd
man/HFLODPlotChr.Rd
man/HostspotsMatrix-class.Rd
man/HostspotsSegments-class.Rd
man/atlas-class.Rd
man/cytobands.Rd
man/dim-fMatrix-method.Rd
man/fMatrix-class.Rd
man/festim.Rd
man/ggQQPlot.Rd
man/glmHBD.Rd
man/glmHBDPlot.Rd
man/hotspot.Rd
man/initialize-HostspotsMatrix-method.Rd
man/initialize-atlas-method.Rd
man/initialize-fMatrix-method.Rd
man/initialize-snpsMatrix-method.Rd
man/initialize-snpsSegments-method.Rd
man/makeAtlasByDistance.Rd
man/makeAtlasByHotspots.Rd
man/makeSubmapByDistance.Rd
man/makeSubmapByHotspots.Rd
man/markerRepresentation.Rd
man/markerSummary.Rd
man/phenoConverter.Rd
man/plotROHSegmentsChr.Rd
man/plotROHSegmentsId.Rd
man/recap.Rd
man/segmentsListByDistance.Rd
man/segmentsListByHotspots.Rd
man/segmentsListSummary.Rd
man/setAlleleFrequencies.Rd
man/setFLOD.Rd
man/setHBDProb.Rd
man/setHBDProbAndFLOD.Rd
man/setHBDProbAndFLODBySnps.Rd
man/setHFLOD.Rd
man/setStatus.Rd
man/setSummary.Rd
man/show-HostspotsMatrix-method.Rd
man/show-HostspotsSegments-method.Rd
man/show-atlas-method.Rd
man/show-fMatrix-method.Rd
man/show-snpsMatrix-method.Rd
man/show-snpsSegments-method.Rd
man/snpsMatrix-class.Rd
man/snpsSegments-class.Rd
man/submapEstim.Rd
man/submapLikelihood.Rd
man/submapSummary.Rd
src/LSE.h
src/RcppExports.cpp
src/forward_backward.cpp
src/likelihood.cpp
src/likelihood_gradient.cpp
src/logEmiss.cpp
src/m4_logEmiss.cpp
src/matrix4.cpp
src/simus.cpp
vignettes/Fantasio.Rmd
vignettes/Fantasio_files/figure-markdown_mmd/fig1-1.png
vignettes/Fantasio_files/figure-markdown_mmd/fig1bis-1.png
vignettes/Fantasio_files/figure-markdown_mmd/fig2-1.png
vignettes/Fantasio_files/figure-markdown_mmd/fig2bis-1.png
vignettes/Fantasio_files/figure-markdown_mmd/fig3-1.png
vignettes/Fantasio_files/figure-markdown_mmd/fig4-1.png
vignettes/Fantasio_files/figure-markdown_mmd/fig4bis-1.png
vignettes/Fantasio_files/figure-markdown_strict/fig1-1.png
vignettes/Fantasio_files/figure-markdown_strict/fig2-1.png
vignettes/Fantasio_files/figure-markdown_strict/fig3-1.png
vignettes/Fantasio_files/figure-markdown_strict/fig4-1.png
