SemDist: Information Accretion-based Function Predictor Evaluation

This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.

AuthorIan Gonzalez and Wyatt Clark
Date of publicationNone
MaintainerIan Gonzalez <gonzalez.isv@gmail.com>
LicenseGPL (>= 2)
Version1.8.0
http://github.com/iangonzalez/SemDist

View on Bioconductor

Files

SemDist/DESCRIPTION
SemDist/NAMESPACE
SemDist/R
SemDist/R/computeIA.R SemDist/R/findRuMi.R SemDist/R/gene2GO.R SemDist/R/utilities.R
SemDist/README.md
SemDist/build
SemDist/build/vignette.rds
SemDist/data
SemDist/data/Info_Accretion_anopheles_BP.rda
SemDist/data/Info_Accretion_anopheles_CC.rda
SemDist/data/Info_Accretion_anopheles_MF.rda
SemDist/data/Info_Accretion_arabidopsis_BP.rda
SemDist/data/Info_Accretion_arabidopsis_CC.rda
SemDist/data/Info_Accretion_arabidopsis_MF.rda
SemDist/data/Info_Accretion_bovine_BP.rda
SemDist/data/Info_Accretion_bovine_CC.rda
SemDist/data/Info_Accretion_bovine_MF.rda
SemDist/data/Info_Accretion_canine_BP.rda
SemDist/data/Info_Accretion_canine_CC.rda
SemDist/data/Info_Accretion_canine_MF.rda
SemDist/data/Info_Accretion_chicken_BP.rda
SemDist/data/Info_Accretion_chicken_CC.rda
SemDist/data/Info_Accretion_chicken_MF.rda
SemDist/data/Info_Accretion_chimp_BP.rda
SemDist/data/Info_Accretion_chimp_CC.rda
SemDist/data/Info_Accretion_chimp_MF.rda
SemDist/data/Info_Accretion_ecolik12_BP.rda
SemDist/data/Info_Accretion_ecolik12_CC.rda
SemDist/data/Info_Accretion_ecolik12_MF.rda
SemDist/data/Info_Accretion_fly_BP.rda
SemDist/data/Info_Accretion_fly_CC.rda
SemDist/data/Info_Accretion_fly_MF.rda
SemDist/data/Info_Accretion_human_BP.rda
SemDist/data/Info_Accretion_human_CC.rda
SemDist/data/Info_Accretion_human_MF.rda
SemDist/data/Info_Accretion_malaria_BP.rda
SemDist/data/Info_Accretion_malaria_CC.rda
SemDist/data/Info_Accretion_malaria_MF.rda
SemDist/data/Info_Accretion_mouse_BP.rda
SemDist/data/Info_Accretion_mouse_CC.rda
SemDist/data/Info_Accretion_mouse_MF.rda
SemDist/data/Info_Accretion_pig_BP.rda
SemDist/data/Info_Accretion_pig_CC.rda
SemDist/data/Info_Accretion_pig_MF.rda
SemDist/data/Info_Accretion_rat_BP.rda
SemDist/data/Info_Accretion_rat_CC.rda
SemDist/data/Info_Accretion_rat_MF.rda
SemDist/data/Info_Accretion_rhesus_BP.rda
SemDist/data/Info_Accretion_rhesus_CC.rda
SemDist/data/Info_Accretion_rhesus_MF.rda
SemDist/data/Info_Accretion_worm_BP.rda
SemDist/data/Info_Accretion_worm_CC.rda
SemDist/data/Info_Accretion_worm_MF.rda
SemDist/data/Info_Accretion_xenopus_BP.rda
SemDist/data/Info_Accretion_xenopus_CC.rda
SemDist/data/Info_Accretion_xenopus_MF.rda
SemDist/data/Info_Accretion_yeast_BP.rda
SemDist/data/Info_Accretion_yeast_CC.rda
SemDist/data/Info_Accretion_yeast_MF.rda
SemDist/data/Info_Accretion_zebrafish_BP.rda
SemDist/data/Info_Accretion_zebrafish_CC.rda
SemDist/data/Info_Accretion_zebrafish_MF.rda
SemDist/data/Parent_Count_anopheles_BP.rda
SemDist/data/Parent_Count_anopheles_CC.rda
SemDist/data/Parent_Count_anopheles_MF.rda
SemDist/data/Parent_Count_arabidopsis_BP.rda
SemDist/data/Parent_Count_arabidopsis_CC.rda
SemDist/data/Parent_Count_arabidopsis_MF.rda
SemDist/data/Parent_Count_bovine_BP.rda
SemDist/data/Parent_Count_bovine_CC.rda
SemDist/data/Parent_Count_bovine_MF.rda
SemDist/data/Parent_Count_canine_BP.rda
SemDist/data/Parent_Count_canine_CC.rda
SemDist/data/Parent_Count_canine_MF.rda
SemDist/data/Parent_Count_chicken_BP.rda
SemDist/data/Parent_Count_chicken_CC.rda
SemDist/data/Parent_Count_chicken_MF.rda
SemDist/data/Parent_Count_chimp_BP.rda
SemDist/data/Parent_Count_chimp_CC.rda
SemDist/data/Parent_Count_chimp_MF.rda
SemDist/data/Parent_Count_ecolik12_BP.rda
SemDist/data/Parent_Count_ecolik12_CC.rda
SemDist/data/Parent_Count_ecolik12_MF.rda
SemDist/data/Parent_Count_fly_BP.rda
SemDist/data/Parent_Count_fly_CC.rda
SemDist/data/Parent_Count_fly_MF.rda
SemDist/data/Parent_Count_human_BP.rda
SemDist/data/Parent_Count_human_CC.rda
SemDist/data/Parent_Count_human_MF.rda
SemDist/data/Parent_Count_malaria_BP.rda
SemDist/data/Parent_Count_malaria_CC.rda
SemDist/data/Parent_Count_malaria_MF.rda
SemDist/data/Parent_Count_mouse_BP.rda
SemDist/data/Parent_Count_mouse_CC.rda
SemDist/data/Parent_Count_mouse_MF.rda
SemDist/data/Parent_Count_pig_BP.rda
SemDist/data/Parent_Count_pig_CC.rda
SemDist/data/Parent_Count_pig_MF.rda
SemDist/data/Parent_Count_rat_BP.rda
SemDist/data/Parent_Count_rat_CC.rda
SemDist/data/Parent_Count_rat_MF.rda
SemDist/data/Parent_Count_rhesus_BP.rda
SemDist/data/Parent_Count_rhesus_CC.rda
SemDist/data/Parent_Count_rhesus_MF.rda
SemDist/data/Parent_Count_worm_BP.rda
SemDist/data/Parent_Count_worm_CC.rda
SemDist/data/Parent_Count_worm_MF.rda
SemDist/data/Parent_Count_xenopus_BP.rda
SemDist/data/Parent_Count_xenopus_CC.rda
SemDist/data/Parent_Count_xenopus_MF.rda
SemDist/data/Parent_Count_yeast_BP.rda
SemDist/data/Parent_Count_yeast_CC.rda
SemDist/data/Parent_Count_yeast_MF.rda
SemDist/data/Parent_Count_zebrafish_BP.rda
SemDist/data/Parent_Count_zebrafish_CC.rda
SemDist/data/Parent_Count_zebrafish_MF.rda
SemDist/data/Term_Count_anopheles_BP.rda
SemDist/data/Term_Count_anopheles_CC.rda
SemDist/data/Term_Count_anopheles_MF.rda
SemDist/data/Term_Count_arabidopsis_BP.rda
SemDist/data/Term_Count_arabidopsis_CC.rda
SemDist/data/Term_Count_arabidopsis_MF.rda
SemDist/data/Term_Count_bovine_BP.rda
SemDist/data/Term_Count_bovine_CC.rda
SemDist/data/Term_Count_bovine_MF.rda
SemDist/data/Term_Count_canine_BP.rda
SemDist/data/Term_Count_canine_CC.rda
SemDist/data/Term_Count_canine_MF.rda
SemDist/data/Term_Count_chicken_BP.rda
SemDist/data/Term_Count_chicken_CC.rda
SemDist/data/Term_Count_chicken_MF.rda
SemDist/data/Term_Count_chimp_BP.rda
SemDist/data/Term_Count_chimp_CC.rda
SemDist/data/Term_Count_chimp_MF.rda
SemDist/data/Term_Count_ecolik12_BP.rda
SemDist/data/Term_Count_ecolik12_CC.rda
SemDist/data/Term_Count_ecolik12_MF.rda
SemDist/data/Term_Count_fly_BP.rda
SemDist/data/Term_Count_fly_CC.rda
SemDist/data/Term_Count_fly_MF.rda
SemDist/data/Term_Count_human_BP.rda
SemDist/data/Term_Count_human_CC.rda
SemDist/data/Term_Count_human_MF.rda
SemDist/data/Term_Count_malaria_BP.rda
SemDist/data/Term_Count_malaria_CC.rda
SemDist/data/Term_Count_malaria_MF.rda
SemDist/data/Term_Count_mouse_BP.rda
SemDist/data/Term_Count_mouse_CC.rda
SemDist/data/Term_Count_mouse_MF.rda
SemDist/data/Term_Count_pig_BP.rda
SemDist/data/Term_Count_pig_CC.rda
SemDist/data/Term_Count_pig_MF.rda
SemDist/data/Term_Count_rat_BP.rda
SemDist/data/Term_Count_rat_CC.rda
SemDist/data/Term_Count_rat_MF.rda
SemDist/data/Term_Count_rhesus_BP.rda
SemDist/data/Term_Count_rhesus_CC.rda
SemDist/data/Term_Count_rhesus_MF.rda
SemDist/data/Term_Count_worm_BP.rda
SemDist/data/Term_Count_worm_CC.rda
SemDist/data/Term_Count_worm_MF.rda
SemDist/data/Term_Count_xenopus_BP.rda
SemDist/data/Term_Count_xenopus_CC.rda
SemDist/data/Term_Count_xenopus_MF.rda
SemDist/data/Term_Count_yeast_BP.rda
SemDist/data/Term_Count_yeast_CC.rda
SemDist/data/Term_Count_yeast_MF.rda
SemDist/data/Term_Count_zebrafish_BP.rda
SemDist/data/Term_Count_zebrafish_CC.rda
SemDist/data/Term_Count_zebrafish_MF.rda
SemDist/data/datalist
SemDist/inst
SemDist/inst/NEWS.Rd
SemDist/inst/doc
SemDist/inst/doc/introduction.R
SemDist/inst/doc/introduction.pdf
SemDist/inst/doc/introduction.rnw
SemDist/inst/extdata
SemDist/inst/extdata/MFO_LABELS_TEST.txt
SemDist/inst/extdata/MFO_PREDS_TEST.txt
SemDist/inst/extdata/mfo_ontology.txt
SemDist/inst/extdata/myIA.rda
SemDist/man
SemDist/man/IAccr.Rd SemDist/man/RUMIcurve.Rd SemDist/man/computeIA.Rd SemDist/man/findRUMI.Rd SemDist/man/parentcnt.Rd SemDist/man/termcnt.Rd
SemDist/vignettes
SemDist/vignettes/introduction.bbl
SemDist/vignettes/introduction.rnw
SemDist/vignettes/refdbshort.bib

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