kobejamescurry
commented
5 years ago in different issues, you give different advice on parameter setting, really confused, can it be automatic to adjust the value inner in function inner?
I have read almost all the issues, too many issues users did not get a good result due to they are not familiar with the setting value of argument, it is really very urgent for the author to give a better suggestion about wgs, wes, panel sequencing., in some of the answer, you just said should be lower or higher, but in more common things, all users use different coverage, so higher or lower just fit for one user. There is really a more detailed doc needed, you will be more free, and people will be more happy using it and in one of the issue, author ignore a basic conception that panel design always contains some chromosome, resulting in the stop of the process, but in your article about one year ago, you write this tool fit for panel sequencing in the abstract, it seems that you should certainly know panel design may not contain all chr sorry for my such words, we all want this package to be one of the best in asan analysis
Sorry, I'm bombarding you with questions... I'd like to make sure my understanding is correct.
Q1: the new code seems to remove the legends. and I found the result format can be used for different sample, a little strange(I post two different paired sample here, one has 75% in purity, no does not have, and the flag is both NULL, the two different paired sample here are wes sample.)
Q2" and I want to know how can I know the precise positon of this cnv(for example, in chr3, chr11 there seems to be a LOH), the most important thing how can I be sure where is a LOH, and does FACETS consider two reasons of LOH(totally delete and heter to homo)
A loss of heterozygosity refers to a loss of one of the parental copies, which may or may not involve a change in total copy number; specifically, some mutation processes lead to a loss of one parental copy accompanied by a simultaneous gain of the other parental copy in the same region, thus leading to a loss of heterozygosity without changing total copy number, aka copy-neutral loss of heterozygosity.
in your table, why 1, 0 i s not a LOH, and (2, 0) means hete to homo, am I right, thanks a lot.
and is dup-loh also a loh? very much thanks, urgent for your reply
this science paper （Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy）use your facets to detect LOH, he defined LOH as following picture. in the result of emcncf() result, you can see I labeled three points, I guess the (1, 0) is a LOH, what about the other two.
what is more, I noticed that two NA in the column mafR.clust, and the corresponding value in column nhet is 0 and 22, I guess it is because nhet is too small, so how should I define the LOH,
here is the corresponding picture of plotSample and logRlogORspider
here is the possible LOH I labeled individual and is the two a LOH
Q3: and do you has some argument value advice for wes, targeted panel, wgs? due to my low ability, I have not found some suggeestions in your doc, thanks a lot
thanks a lot
here is another sample