TMB | 肿瘤突变负荷学习笔记(tumor mutation burden) | Genomics library
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kandi X-RAY | TMB Summary
肿瘤突变负荷学习笔记(tumor mutation burden)
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Top functions reviewed by kandi - BETA
- Run germline calling .
TMB Key Features
TMB Examples and Code Snippets
TMB的定义如下:TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome examined. 可参考文献[1]
panel size的问题对于TMB的计算很重要,不能太小,最小0.5吧,也有建议0.8以上,不过总的结论是不能太小,越大越接近外显子的结果.
panel的设计初衷有时候不仅仅是call变异,也有SV、基因融合等等,
根据文献[1,8]stop-gain mutations in tumor suppressor gene 应该去掉,以下两个数据库有基因的分类
Oncokb database: https://oncokb.org/cancerGenes
cosmic database: https://cancer.sanger.ac.uk/census#cl_search
下载最新的dbsnp
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/
这里的germline位点(SAO=1)和common位点(COMMON=1),这里common SNP is one that has at least one 1000Genomes population with a MAF >= 1% and for which 2 or more founders contribute to
Community Discussions
Trending Discussions on TMB
QUESTION
I have been struggling with this for hours without any result :(. I have a select string command which finds various strings in the files
...ANSWER
Answered 2021-Jun-04 at 03:40This should do, I'm just not sure of what the source type object types are for the variables holding the values.
QUESTION
I am trying to write a sorting algorithm for sorting filesizes intelligently regardless of the input format. My function is supposed to sort an array of string inputs to give required outputs like so;
...ANSWER
Answered 2021-May-14 at 08:29QUESTION
I am using the glmmTMB library to run mixed models, within a R markdown document. Any model that I run, I get these warnings:
...ANSWER
Answered 2021-Apr-17 at 16:34It's harmless. You can:
- ignore it
- use
suppressWarnings()
(at the possible cost of missing other relevant warnings!) - install the development version from GitHub, where it was fixed in this commit. (The binary packages on the repository have also been updated now.)
- wait for a new version of glmmTMB to make it to CRAN (hopefully in the next few weeks ...)
or you could downgrade your version of Matrix
to an older version (using remotes::install_version()
or the snapshot
package)
QUESTION
I am trying to create Ajax logging feature for elFinder so I added event handlers:
...ANSWER
Answered 2021-Mar-23 at 15:02Because the path encoding method can be changed with the volume driver, the client side does not implement a function to decode it.
However, if it is the default encoding method, it can be decoded as follows.
QUESTION
Using dat
(found here), I run the following model:
ANSWER
Answered 2021-Mar-16 at 03:40I'm going to answer your questions in reverse order:
- The
plot_model()
function calls functions from theggeffects
package. Specifically,ggpredict()
does a lot of the work. If you go to the following URL, you will find lots of information on how to alter effects plots and getting all sorts of information from the fitted model.
https://cran.r-project.org/web/packages/ggeffects/vignettes/ggeffects.html
- I don't really agree that the interaction does not look significant. The confidence interval doesn't overlap with the other categories mean for the majority of the plot. That might be beside the point, however, as you are currently plotting categorical data in a manner that makes it look continuous. This does not change how the model is being fit under the hood, but it changes the default behaviour of
sjPlot
. I have fit the model you specified with factors and plotted it how I think it should be plotted below. I don't think this changes much about the plot, but it might change your interpretation. The difference shown here in this plot is consistent with the model summary output and can be stated like this: the difference between the two levels ofpost
is not the same wheness
is a 0 vs. a 1. Also, see how the CIs of the twoess
categories overlap with the mean whenpost
is 0 but they are significantly different whenpost
is 1.
Let me know if any of this requires further clarification.
QUESTION
I want to create a .xml file with an specific config, this config needs an hostname and ip, i have created the hosts.csv
to input this data being them vm-tmb-test1;127.0.0.1
on .csv file
for each separator line ";"
is a hostname and ip of a server, but the looping i have created print for each ip in the hosts.csv
Code Structure
...ANSWER
Answered 2021-Mar-11 at 19:49A single GNU sed
call could do the job:
QUESTION
i have created a slackbot with nodejs using @slack/bolt
.
i'm able to receive event in my nodejs server from slack whenever i tag with my slackapp and send textMessage or textMessage+Fileattachment. Please find the nodejs source code and output of the event object below.
The problem is, when i upload a file in slack, the event is received by my nodejs slack-bot
. (shown in below screenshot+view the event object details in the output attached below)
- The links to the uploaded file is retrieved by the nodejs slack-bot from the event object
- i'm able to use the link in web browser(for eg. google chrome) to view the uploaded file.
- When i use the link to download the file via nodejs code, the file gets downloaded, but the downloaded file is corrupted
i'm not sure how to download the valid file using nodejs slack-bot. i have tried changing few parameters and settings but no success. The docs aren't helping me so far
Please help me out
...Nodejs source code
ANSWER
Answered 2021-Feb-19 at 13:00- The issue was due to the type of token passed to the file download api
BOT_TOKEN
is the appropriate token that has to be passed to the file download api- Issue got fixed once i passed the
BOT_TOKEN
to the file download api
Below is the logic to download the file that was uploaded in slack
QUESTION
Context: I am running a simulation via R that each repetition takes too long and it is memory consuming. Therefore, I need that for every repetition another session in R starts, so that I will not run into memory issues.
My problem: After executing my bash script, I exit
from the terminal, the current repetition finishes successfully, but the next one does not start (I am running it on a server via ssh
).
What I have done:
compoisson.sh
bash script:
ANSWER
Answered 2021-Feb-09 at 20:23Solved with nohup ./compoisson.sh &
instead of sh compoisson.sh &
QUESTION
I'm a beginner with python. I've created a little program for my navigation homework which when I input the data solves it for me but it's not working. It asks the initial question to determine which type of problem to solve and then, when it's supposed to solve it, it crashes. Why is that?
...ANSWER
Answered 2021-Jan-28 at 11:47Input in python receives the value as string, and you are comparing it to integer value in your if condition
update your input statement to the following line to receive integer input:
QUESTION
I'm struggling to move an element into the next element in the DOM. I can move it but it keeps repeating itself into the other div's with the same class.
This is my HTML:
...ANSWER
Answered 2021-Jan-07 at 12:06To achieve this you could loop through all p
elements as there are multiple, and then use appendTo()
to add them to their related .tmb
. Try this:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install TMB
You can use TMB like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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