Closed Aimee2018 closed 1 year ago
Hi @Aimee2018
BSgenome.Hsapiens.UCSC.hg38
, please install the package with BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
firstly.@Aimee2018 Any feedback?
Hi,Thanks a lot for you detailed reply!Meanwhile, I still have some questions and problems to consult you.
I have read your paper(Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes). I have some questions: 1) How do you transform 8 copy number features into 80 copy number components. why is it 80? 2) In your paper, a clear claim: each of the predefined 80 copy number components has clear and fixed biological meaning. How do you find and define the fixed biological meaning connected to your 80 copy number components? 3) In the "Mutational processes underlying copy number signatures" part, you give a TDP score. what is the meaning of high or low score? How do you know it is a tandem duplication just according to CNV data?
Can sigminer support detect the HRD or not?
what is the differences between sigminer and signature.tools.lib (https://github.com/Nik-Zainal-Group/signature.tools.lib)
Thank you for you time!
------------------ 原始邮件 ------------------ 发件人: "ShixiangWang/sigminer" @.>; 发送时间: 2022年10月17日(星期一) 晚上9:50 @.>; @.**@.>; 主题: Re: [ShixiangWang/sigminer] signature and reference version problem (Issue #419)
@Aimee2018 Any feedback?
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@Aimee2018 Thanks for your questions, please read the following reply.
sigminer
provides such approach, you can check https://github.com/ShixiangWang/sigminer/blob/master/data-raw/CN-features.R to know how the 80 components generated. You can provide you own setting by modifying the option at https://github.com/ShixiangWang/sigminer/blob/95958d14821f862c52e7141daba17c2ba20daf7d/R/sig_tally.R#L149
b. Given the components below, you can easily understand that BP10MB[2]
indicates 2 breakpoints per 10 MB region, this is a fixed meaning however, this cannot be reflected by the previous approach (Nat. Genetics, 2018), which uses a flexmix model to extract the components, if it labels a component as BP10MB[2]
, it does not mean the same thing, instead, it may represent a poison distribution with mean 1.5, and if you input different data, the parameter of this distribution may change, and even the number of components will change.> sigminer::CN.features
feature component label min max
1: BP10MB BP10MB[0] point 0 0
2: BP10MB BP10MB[1] point 1 1
3: BP10MB BP10MB[2] point 2 2
4: BP10MB BP10MB[3] point 3 3
5: BP10MB BP10MB[4] point 4 4
6: BP10MB BP10MB[5] point 5 5
7: BP10MB BP10MB[>5] range 5 Inf
8: BPArm BPArm[0] point 0 0
9: BPArm BPArm[1] point 1 1
10: BPArm BPArm[2] point 2 2
11: BPArm BPArm[3] point 3 3
12: BPArm BPArm[4] point 4 4
13: BPArm BPArm[5] point 5 5
This was reflected in a supp figure:
c. For scoring related question, please check https://shixiangwang.github.io/sigminer/reference/scoring.html.
I am closing it now. Feel free to reopen if you have further questions.
Hi, when I used sigminer, I met some problems.
mats <- mt_tally <- sig_tally( laml, ref_genome = "BSgenome.Hsapiens.UCSC.hg38", useSyn = TRUE, mode = "ALL" )