Can't make lolliplot from my vcf file

[spereyra]

Hey there, I am trying to make a lolliplot from data from a vcf file. Everything works nicely when following the example from 4.13 in the vignette, but not on my own data. When running the lolliplot command, it returns this error message:

> lolliplot(mutation.frequency, features, ranges=elocsVCFgr[3])
Error in combine_CompressedList_objects(class(x), objects, use.names = FALSE,  : 
  the objects to combine must be CompressedList objects (or NULLs)

Can you help me figure out what does this error means? A google search yielded no insight on this... Thank you.

[jianhong]

HI Silvana,

Thank you for reporting the error. Could you please send me the minimized files and codes to repeat your error? Thanks.

Jianhong.

On Thu, Oct 18, 2018 at 10:49 AM Silvana Pereyra notifications@github.com wrote:

Hey there, I am trying to make a lolliplot from data from a vcf file. Everything works nicely when following the example from 4.13 in the vignette, but not on my own data. When running the lolliplot command, it returns this error message:

lolliplot(mutation.frequency, features, ranges=elocsVCFgr[3]) Error in combine_CompressedList_objects(class(x), objects, use.names = FALSE, : the objects to combine must be CompressedList objects (or NULLs)

Can you help me figure out what does this error means? A google search yielded no insight on this... Thank you.

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-- Yours sincerely, Jianhong Ou

[spereyra]

Sorry for the delay and thank you for your reply. Here is my code and my minimized vcf. vcf_elocsVCF_s.vcf.gz

vcf_elocsVCF_s <- readVcf("vcf_elocsVCF_s.vcf")
elocsVCFgr <- GRanges("4", IRanges(164445450, 165305202, names="MARCH1"))

mutation.frequency <- rowRanges(vcf_elocsVCF_s)
mcols(mutation.frequency) <- cbind(mcols(mutation.frequency), 
                                   VariantAnnotation::info(vcf_elocsVCF_s))
## plot Global Allele Frequency based on AC/AN
mutation.frequency$score <- mutation.frequency$AF*100
seqlevelsStyle(elocsVCFgr) <- seqlevelsStyle(mutation.frequency) <- "UCSC" 
trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                         org.Hs.eg.db,
                         gr=elocsVCFgr)
features <- c(range(trs[[1]]$dat), range(trs[[3]]$dat))
names(features) <- c(trs[[1]]$name, trs[[3]]$name)
features$fill <- c("lightblue", "mistyrose")
features$height <- c(.02, .04)
lolliplot(mutation.frequency, features, ranges=elocsVCFgr)

[jianhong]

this bug should be fix in newest development version.

On Mon, Oct 29, 2018 at 2:50 PM Silvana Pereyra notifications@github.com wrote:

Sorry for the delay and thank you for your reply. Here is my code and my minimized vcf. vcf_elocsVCF_s.vcf.gz https://github.com/jianhong/trackViewer/files/2526636/vcf_elocsVCF_s.vcf.gz

vcf_elocsVCF_s <- readVcf("vcf_elocsVCF_s.vcf") elocsVCFgr <- GRanges("4", IRanges(164445450, 165305202, names="MARCH1"))

mutation.frequency <- rowRanges(vcf_elocsVCF_s) mcols(mutation.frequency) <- cbind(mcols(mutation.frequency), VariantAnnotation::info(vcf_elocsVCF_s))

plot Global Allele Frequency based on AC/AN

mutation.frequency$score <- mutation.frequency$AF*100 seqlevelsStyle(elocsVCFgr) <- seqlevelsStyle(mutation.frequency) <- "UCSC" trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, gr=elocsVCFgr) features <- c(range(trs[[1]]$dat), range(trs[[3]]$dat)) names(features) <- c(trs[[1]]$name, trs[[3]]$name) features$fill <- c("lightblue", "mistyrose") features$height <- c(.02, .04) lolliplot(mutation.frequency, features, ranges=elocsVCFgr)

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-- Yours sincerely, Jianhong Ou

[spereyra]

That's great! Thank you!