Error message

[zenglongjin]

Dear Reimand:
After we add the final 16834 line: chr3 12146056 12147096 (previous 16833 lines did not report an error), we got a strange message as following:
Error in RM2(maf = muts, sites = ctcf_chr3_4, window_size = window_size) : Error in .width_as_unnamed_integer(width, msg = "an end that is greater or equal to its start minus one") : each range must have an end that is greater or equal to its start minus one

Thank you very much for your attention and consideration.

chr | start | end
1 chr1 | 843081 | 843977
...
16833 chr3 | 12138282 | 12139593
16834 chr3 | 12146056 | 12147096**

[reimand0]

Hi Zenglongjin, thanks for reporting. I was not able to reproduce this error by adding that last site to the sites shown in the example on my github (object ctcf_chr3_4). ctcf_chr3_4 = rbind(ctcf_chr3_4, data.frame(chr="chr3", start=12146056, end=12147096, stringsAsFactors= FALSE)) window_size = 25 results2 = RM2(maf = muts, sites = ctcf_chr3_4, window_size = window_size) results2 # mut_type pp this_coef obs_mut exp_mut exp_mut_lo #1 total_muts__total_muts 9.175249e-11 0.5609654 274 199 172 # exp_mut_hi fc pp_cofac this_coef_cofac n_sites_tested # 1 227 1.376884 NA NA 7195 One potential solution: perhaps there is another site in your dataset that duplicates the region chr3:12146056-12147096 or overlaps it partially, causing this error. In RM2, site midpoints are derived, then the sites are extended in both directions by fixed sequence length, and then all sites are merged. I hope this helps! Jüri

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On Sat, Oct 30, 2021 at 7:47 AM zenglongjin ***@***.***> wrote: Dear Reimand: After we add the final 16834 line: chr3 12146056 12147096 (previous 16833 lines did not report an error), we got a strange message as following: Error in RM2(maf = muts, sites = ctcf_chr3_4, window_size = window_size) : Error in .width_as_unnamed_integer(width, msg = "an end that is greater or equal to its start minus one") : each range must have an end that is greater or equal to its start minus one Thank you very much for your attention and consideration. chr | start | end 1 chr1 | 843081 | 843977 ... 16833 chr3 | 12138282 | 12139593 16834 chr3 | 12146056 | 12147096** — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETAF7ICEDDQV7HAKDO7AUDUJPLLNANCNFSM5HA7ZJ6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[zenglongjin]

Dear Reimand:
After testing it, I found that mutational data had duplicate fragments, along with an new error that prevented the package from running smoothly when doing function: cbind(mutations_chr3_4,get_mut_trinuc_strand(mutations_chr3_4)).
The error as following:
Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr5"
Thank you very much for your attention and consideration.

[reimand0]

OK, this makes sense. One of the sites or mutations is very close to the end of Chr5. Sometimes this could happen when GRCH38 and GRCH37 are mixed up.

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On Sat, Oct 30, 2021 at 10:17 AM zenglongjin ***@***.***> wrote: Dear Reimand: After testing it, I found that mutational data had duplicate fragments, along with an new error that prevented the package from running smoothly when doing function: *cbind(mutations_chr3_4,get_mut_trinuc_strand(mutations_chr3_4))*. The error as following: Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr5" Thank you very much for your attention and consideration. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETAF7OASIXRBKISZ4VVQXLUJP46TANCNFSM5HA7ZJ6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[zenglongjin]

Dear Reimand:
Your suggestion is helpful, while we noticed the NCBI_Build=='GRCH38' in mutational data downloaded by TCGAbiolinks-mutect2 pipeline. We don't know how to discern the accuracy of TCGAbiolinks, perhaps further improvements are necessary.
Thank you very much for your attention and consideration.

[reimand0]

ok, I'm glad it helped. I will close this issue now. Please feel free to get in touch again.