User: Chao-Jen Wong
Chao-Jen Wong • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- USA/Seattle/Fred Hutchinson Cancer Research Center
- Last seen:
- 1 year, 3 months ago
- Joined:
- 3 years, 7 months ago
- Email:
- c****@fredhutch.org
Posts by Chao-Jen Wong
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... Thanks a lot. I did not know that. ha......
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written 15 months ago by
Chao-Jen Wong • 30
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... FYI, I use makeTxDbFromBiomart() instead and get the right gene IDs and transcripts. However, the metadata was wrong due to error detected by .Ensembl_getMySQLCoreDir(), which is not a big deal. sessionInfo() is the same as above. Thanks.
> txdb <- makeTxDbFromBiomart(biomart="ENSEMBL_MAR ...
written 15 months ago by
Chao-Jen Wong • 30
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... As I was using the TxDb.Mmusculus.UCSC.mm10.ensGene package installed using biocLite(), the ID appears to be neither Eensembl ID nor EntrezID. I believe those gene IDs are wrong. (I am using Bioconductor 3.5 on R/3.4, and all the packages are just updated. see sessionInfo() below.)
> library(Tx ...
written 15 months ago by
Chao-Jen Wong • 30
• updated 15 months ago by
James W. MacDonald ♦ 46k
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... Hi, Michael,
I just pileup() and it seems to work for my purpose. I parse the return the data.frame of pileup() and compare with the reference genome to define the type of mismatch. I have not tried tallyVariants(), but it sounds even better. I will definitely try it tomorrow. Thanks for the help ...
written 17 months ago by
Chao-Jen Wong • 30
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... Hi, bioconductor members,
I have two questions here. The first one is basically about how to use narrow() to keep the wanted sequence in an efficient way. I have a read and corresponding cigar, a subset from my GAlignments instance. I want to clip the insertion and soft-clip from the read so that ...
written 17 months ago by
Chao-Jen Wong • 30
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... Thank you, Michael, for the helpful details. Converting with grglist() using drop.D.ranges=TRUE before calling findoverlaps() would definitely work for my case. Wouldn't have known this before.
Thanks,
CJ
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written 17 months ago by
Chao-Jen Wong • 30
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... The results if using R/devel & Bioconductor 3.4.
> sessionInfo()
R Under development (unstable) (2016-12-19 r71815)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_ ...
written 18 months ago by
Chao-Jen Wong • 30
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... Hi guys,
My task is to find the width of intersect areas of GAlignments reads and GRanges objects. First, I have made sure that there are overlapping for at least 1L by using findOverlaps() and then use pintersect() and width() to find the width of the overlapping area. For my case, I have a splic ...
written 18 months ago by
Chao-Jen Wong • 30
• updated 18 months ago by
Michael Lawrence ♦ 10.0k
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... Thanks a lot for making the changes!
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written 18 months ago by
Chao-Jen Wong • 30
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... There is a bioconductor package "MLInterfaces" that contains interfaces to R machine learning procedures such as svm, random forest, knn, and etc. Those procedures are built for general purpose, yet you might find it quite helpful for expression data.
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written 19 months ago by
Chao-Jen Wong • 30
Latest awards to Chao-Jen Wong
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Combining .idat and GEO data sets in minfi
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