anno.orgHs: annotation for translating between gene identifiers

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

Table for translating between Ensembl, NCBI Entrez and HGNC symbol human gene identifiers. Gene biotype, exonic gene length and proportion GC-bases are also included. For more exhaustive annotation including gene names, GO terms and so on, please refer to R Bioconductor packages AnnotationDbi and org.Hs.eg.db.

Usage

anno.orgHs

Format

An object of class data.frame with 58219 rows and 7 columns.

Details

Data is from GENCODE v26/GRCh38.p10. with NCBI Entrez identifiers matched using HGNC symbol against org.Hs.eg.db package.

References

Carlson M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.7.0.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760-74.

See Also

fromTo, org.Hs.eg.db

Examples

head(anno.orgHs)
dim(anno.orgHs)
colSums(apply(anno.orgHs, 2, is.na))
colSums(!apply(anno.orgHs[,1:4], 2, duplicated))
# some extremes
anno.orgHs[which.max(anno.orgHs$length),]
anno.orgHs[which.min(anno.orgHs$length),]
anno.orgHs[which.max(anno.orgHs$GC),]
anno.orgHs[which.min(anno.orgHs$GC),]
attributes(anno.orgHs)$genome

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.