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.

Author
Ian Gonzalez and Wyatt Clark
Date of publication
None
Maintainer
Ian Gonzalez <gonzalez.isv@gmail.com>
License
GPL (>= 2)
Version
1.8.0
URLs

View on Bioconductor

Man pages

computeIA
Compute information accretion for an ontology
findRUMI
Information accretion based predictor assessment
IAccr
Information Accretion Data
parentcnt
Parent Count Data
RUMIcurve
Information accretion based predictor assessment (across many...
termcnt
Term Count Data

Files in this package

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