IAccr: Information Accretion Data

In SemDist: Information Accretion-based Function Predictor Evaluation

Description

This data set contains the information accretion values for each term in the requested ontology/species.

Usage

IAccr

Format

A named numeric vector with one value corresponding to each GO accession in the ontology.

Source

The gene ontology data was obtained from the GO.db package and the annotation data was obtained from the following packages for each organism:

anopheles = org.Ag.eg.db

arabidopsis = org.At.tair.db

bovine = org.Bt.eg.db

canine = org.Cf.eg.db

chicken = org.Gg.eg.db

chimp = org.Pt.eg.db

ecolik12 = org.EcK12.eg.db

fly = org.Dm.eg.db

human = org.Hs.eg.db

malaria = org.Pf.plasmo.db

mouse = org.Mm.eg.db

pig = org.Ss.eg.db

rat = org.Rn.eg.db

rhesus = org.Mmu.eg.db

worm = org.Ce.eg.db

xenopus = org.Xl.eg.db

yeast = org.Sc.sgd.db

zebrafish = org.Dr.eg.db

Examples

data("Info_Accretion_mouse_CC", package = "SemDist")
str(IAccr)

Example output

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GO.db

Loading required package: annotate
Loading required package: XML
 Named num [1:1320] 4.57 6.11 2.7 2.98 0 ...
 - attr(*, "names")= chr [1:1320] "GO:0000015" "GO:0000109" "GO:0000110" "GO:0000118" ...

SemDist documentation built on Nov. 8, 2020, 8:27 p.m.