I am using the following code to retrieve the exon sequences of gene Tcfap2b with GeneID:21419. There are 8 exons for this gene.


for (i in sequence(50)) {
+ x <- getSequence(id=21419,type="entrezgene",seqType="gene_exon",mart=ensembl)
+ if (is.null(x)) print('NULL result')
+ if (!is.null(x)) print("Correct result")
+ }

This gives 44 NULL results and 6 correct results. 'correct' means getSequence() outputs the sequences of the exons.

> sessionInfo()
R version 2.8.1 (2008-12-22) 
x86_64-pc-linux-gnu 

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_1.16.0

loaded via a namespace (and not attached):
[1] RCurl_0.94-0 XML_1.99-0   tools_2.8.1

Thank you,

Juerg Straubhaar, Umass Med School

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