Question

CustomproDB JunctionType function

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Entering edit mode

georges.bedran • 0

@georgesbedran-11010

Last seen 6.7 years ago

hello,

i'm currently working on a proteogenomics project, and i am using customProDB to generate a custom DB, it's a great R package and i find it really helpful.

During the process and while trying to generate my novel junctions peptides fasta, I believe that I ran into a little bug.

at line 131 in the function JunctionType.R "if(length(index_NA) >= 0) matchid_new <- matchid[-index_NA, ]" the if condition will have a true value either if (length(index_NA) is equal to or greater than 0, in the case when (length(index_NA) is equal to 0, R is returning a null value for matchid_new, thus returning a wrong list of jun_type.

for example, in my case it was giving me a list full of junctions that connect 2 known exons (97000 junctions that connect 2 known exons).

and after changing the code to :

if(length(index_NA) > 0) matchid_new <- matchid[-index_NA, ]

else {matchid_new <- matchid}

i got a list of 95000 known junctions and 2000 new alternative splicing junctions.

i am using R version 3.3.0 and customProDB version 1.10.0

thank you.

customprodb • 1.2k views

ADD COMMENT • link updated 8.5 years ago by xiaojing.wang ▴ 50 • written 8.5 years ago by georges.bedran • 0

score 0 · Answer 1 · 2016-06-30

Thanks for pointing this out. It must be a typo. I’ll update the package soon. Xiaojing From: georges.bedran [bioc] [mailto:noreply@bioconductor.org] Sent: Thursday, June 30, 2016 5:51 AM To: Wang, Xiaojing <xiaojing.wang@vanderbilt.edu> Subject: [bioc] CustomproDB JunctionType function Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User georges.bedran<https: support.bioconductor.org="" u="" 11010=""/> wrote Question: CustomproDB JunctionType function<https: support.bioconductor.org="" p="" 84473=""/>: hello, i'm currently working on a proteogenomics project, and i am using customProDB to generate a custom DB, it's a great R package and i find it really helpful. During the process and while trying to generate my novel junctions peptides fasta, I believe that I ran into a little bug. at line 131 in the function JunctionType.R "if(length(index_NA) >= 0) matchid_new <- matchid[-index_NA, ]" the if condition will have a true value either if (length(index_NA) is equal to or greater than 0, in the case when (length(index_NA) is equal to 0, R is returning a null value for matchid_new, thus returning a wrong list of jun_type. for example, in my case it was giving me a list full of junctions that connect 2 known exons (97000 junctions that connect 2 known exons). and after changing the code to : if(length(index_NA) > 0) matchid_new <- matchid[-index_NA, ] else {matchid_new <- matchid} i got a list of 95000 known junctions and 2000 new alternative splicing junctions. i am using R version 3.3.0 and customProDB version 1.10.0 thank you. ________________________________ Post tags: customprodb You may reply via email or visit CustomproDB JunctionType function