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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SemDist")
AuthorIan Gonzalez and Wyatt Clark
Bioconductor views Annotation Classification GO Software
Date of publicationNone
MaintainerIan Gonzalez <gonzalez.isv@gmail.com>
LicenseGPL (>= 2)
Version1.10.0
http://github.com/iangonzalez/SemDist

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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