check if input BED file is correctly formatted

[borauyar]

If the BED file doesn't follow the specifications or contains incomplete columns (e.g. missing the "name" field), some functions may fail (e.g. queryGff).

[aoiwaka]

Hi,

I've been running into an issue about this. I was able to run the script for summarizing overlaps with queryGFF on R yesterday however, when I try to execute the exact same script I now get this error:

Error: subscript is a NSBS object that is incompatible with the current subsetting operation

After some Googling, I tried editing my .gtf file so that the first column lists the chromosome number as "chr1" instead of just "1". This seemed to have help as I was able to execute queryGFF, except I now end up with a dataframe that has everything except for queryIndex, queryRange, query_name, and query_score. Instead it lists overlappingQuery (which I believe is the same as "queryRange"). I also checked my bed file and added the "name" field, which were just numbers 1 to n number of lines however, this didn't help and I end up with the same result. This is an issue since I don't know how I'll be able to select unique queries without the queryIndex.

So, my question is: did RCAS undergo an update just yesterday that changed the queryGFF function? I'm wondering this because I literally had no problem running the commands in the vignette for displaying targeted gene types and now today when I try running the same exact commands I end up with an error. I also didn't update anything on R studio between yesterday and today (at least to my knowledge, consciously).

Thanks!
Aoi

[borauyar]

Dear Aoi,
Sorry for the late response. No, I haven't made an update to RCAS, however, some dependencies of RCAS may have had updates that might affect the behaviour of RCAS functions.
Would it be possible for you to send me a test case so that I can reproduce the issue here?
Do you get this error with the built-in test data in RCAS as well?
Bora

[aoiwaka]

Hi Bora, Thanks for your message! Yeah, I figured there were some updates to some of the dependencies...I reanalyzed my eCLIP data just now using RCAS and was able to run everything smoothly again. So, whatever issues there were on some of the packages it seems to have resolved itself. Thanks! Aoi From: Bora Uyar ***@***.***> Reply-To: BIMSBbioinfo/RCAS ***@***.***> Date: Monday, January 24, 2022 at 4:29 AM To: BIMSBbioinfo/RCAS ***@***.***> Cc: "Wakabayashi, Aoi" ***@***.***>, Comment ***@***.***> Subject: [External] Re: [BIMSBbioinfo/RCAS] check if input BED file is correctly formatted (#13) Dear Aoi, Sorry for the late response. No, I haven't made an update to RCAS, however, some dependencies of RCAS may have had updates that might affect the behaviour of RCAS functions. Would it be possible for you to send me a test case so that I can reproduce the issue here? Do you get this error with the built-in test data in RCAS as well? Bora — Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APAIVU7XDMOHDDYW2VIV57LUXULXHANCNFSM47IQJUTA>. 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>. You are receiving this because you commented.Message ID: ***@***.***>

[borauyar]

@aoiwaka Great! Thanks for letting me know.