Checks mapping efficiency for IDs on the most commonly used ID types

Checks mapping efficiency for IDs on the most commonly used ID types

checkIDmappingEfficiency(IDs, keytype, db = org.Hs.eg.db)

Arguments

IDs	character vector of IDs
keytype	corresponding keytype
db	database object, default org.Hs.eg.db

Value

Returns a data.frame containing information of mapping efficiency on GO, ENTREZ and KEGG IDs

Examples

library(org.Hs.eg.db)
#> Loading required package: AnnotationDbi
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: parallel
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#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:parallel':
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#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from 'package:stats':
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#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#>     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#>     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#>     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#>     union, unique, unsplit, 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
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#> Attaching package: 'S4Vectors'
#> The following objects are masked from 'package:base':
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#> Attaching package: 'IRanges'
#> The following object is masked from 'package:grDevices':
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#>     windows
data("exampleContrastData", package = "prora")
df <- get_UniprotID_from_fasta_header(exampleContrastData)
checkIDmappingEfficiency(df$UniprotID, keytype = "UNIPROT")
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#>                InputIDs  ENTREZIDs    KEGGIDs      GOIDs
#> Number             3701 3680.00000 1534.00000 3660.00000
#> Percent Mapped      100   99.43259   41.44826   98.89219