Errors found in chapter 9

[ezjung]

R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

p314

export(pseudogene_sample, con="five_random_pseudogene.gtf", format="GTF"))

bed_data <- pseudogene_sample

p315

promoters() function extract 2000 upstream, not 3000

p316

"BSgenome.Mmusculus.UCSC.mm10" file size is 600.2MB

p323

amy1_tx object should be assigned before amy1_exons. Rearrange of the paragraph needed. amy1_tx coding chunk should preced amy1_exons

Easier way may be:

amy1_txid <- amy1$tx_id  # vector of tx_id
mm_exons[amy1_txid] # This should produce list of GRanges object by the transcripts

Error with psetdiff(), seemed psetdiff() no longer supported by GRangesList instance. Used setdiff() and worked fine.

p324

psetdiff is not working any more. Used setdiff

p326

My number is as below,

> length(unique(queryHits(hits)))
[1] 57623
> length(unique(queryHits(hits)))/length(dbsnp137_resized)
[1] 0.02134185

difference is small enough, but please check it again

In the end of paragraph of this page,
"...the number of unique query hits in this Hits object: 118,594."
where is 118,594 came from? It should be 58343(or 57623)

p327

Code works but number is diffrent from the number produced with my system. Please double check if the number is right