Hi there,

I was using the R scripts written by Irsan(https://www.biostars.org/p/83901/) to obtain the exonic length for each protein-coding gene. However, the length information of many genes were not included in the final output. I randomly picked some of them and found that if I manually get the ensembl_transcript_id from biomaRt then the exonsBy() function works well. Could anybody tell me why? The scripts are pasted below:

library(biomaRt)
library(GenomicFeatures)
txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl")
exons.list.per.gene <- exonsBy(txdb2, by="gene")   
exonic.gene.length <- lapply(exons.list.per.gene, function(x){sum(width(reduce(x)))})

### The results obtained from the code above do not contain length information for "ENSG00000281887" (randomly picked as an example). But I can manually run to get the exonic length. ###

mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
res <- getBM(attributes=c("ensembl_gene_id", "ensembl_gene_id_version", "ensembl_transcript_id",
                    "hgnc_symbol"), filters="ensembl_gene_id", values="ENSG00000281887", mart=mart)
txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl", transcript_ids=res$ensembl_transcipt_id)
exons.list.per.gene <- exonsBy(txdb2, by="gene")   
exonic.gene.length <- lapply(exons.list.per.gene, function(x){sum(width(reduce(x)))})   

I know I could run the script in a loop to get the gene length information for each gene, but it takes too much time since the "makeTxDbFromBiomart" is extremely slow.  Any suggestions would be really appreciated.

Making the TxDb when there is already one available is unnecessary effort duplication. Johannes Rainer has already made EnsDb packages for human, and put them on the AnnotationHub.

> library(AnnotationHub)

Attaching package: 'AnnotationHub'

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

    cache

> hub <- AnnotationHub()
snapshotDate(): 2017-04-25
> query(hub, c("ensdb","homo sapiens"))
AnnotationHub with 2 records
# snapshotDate(): 2017-04-25
# $dataprovider: Ensembl
# $species: Homo Sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53211"]]'

            title                            
  AH53211 | Ensembl 87 EnsDb for Homo Sapiens
  AH53715 | Ensembl 88 EnsDb for Homo Sapiens
> z <- hub[["AH53715"]]
require("ensembldb")
downloading from 'https://annotationhub.bioconductor.org/fetch/60453'
retrieving 1 resource
  |======================================================================| 100%
> exs <- exonsBy(z, "gene")
exs[["ENSG00000281887"]]
> GRanges object with 6 ranges and 1 metadata column:
      seqnames                 ranges strand |         exon_id
         <Rle>              <IRanges>  <Rle> |     <character>
  [1]        7 [150716668, 150716690]      + | ENSE00003762946
  [2]        7 [150719042, 150719090]      + | ENSE00003720568
  [3]        7 [150720048, 150720406]      + | ENSE00003728945
  [4]        7 [150737505, 150737708]      + | ENSE00003747063
  [5]        7 [150740879, 150740927]      + | ENSE00003728722
  [6]        7 [150742183, 150743646]      + | ENSE00003751629
  -------
  seqinfo: 389 sequences from GRCh38 genome
> length(exs)
[1] 64592

Thanks very much! It perfectly solved my problem!