User: cannilay

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cannilay20
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Posts by cannilay

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Manhattan Plot in R with non-numeric CHR values
... Solved. I used this [GGplot2 Manhattan Plot Function][1]. Thanks to authors! [1]: https://github.com/pcgoddard/Burchardlab_Tutorials/wiki/GGplot2-Manhattan-Plot-Function ...
written 7 months ago by cannilay20
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Comment: C: Manhattan Plot in R with non-numeric CHR values
... qqman does not seem feasible since I have ~ thousands unique scaffold names.. But if you still know a better way to use qqman for so many chr's, I am open any suggestions. ...
written 7 months ago by cannilay20
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Manhattan Plot in R with non-numeric CHR values
... Hello, I have a plenty of scaffold and contig names which are non-numeric like Scaffold1 (or any other name. That's why I cannot replace them with number since I have names like Fvb1 etc) instead of "1". So, can somebody offer a package in R to get Manhattan plots with non-numeric chromosome ident ...
R ewas manhattan plot gwas written 7 months ago by cannilay20 • updated 7 months ago by bernatgel2.6k
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Comment: C: How to extract filename and change text in the same file
... deleted my comment since it is solved ...
written 7 months ago by cannilay20
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Comment: C: How to Turn Multiple ALT alleles to Genotype Calls
... did not work xd Can you share the solution if you have? If I use the command below to divide them into biallelic, it does not work correctly. Another solution is maybe to get rid of them but I do not lean towards.. Would be appreciated if you share the solution. Thanks! ...
written 7 months ago by cannilay20
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Comment: C: SnpMatrix from VCF file
... What will you do in multiallelic cases? I have some GT values like 3/3, 1/2, 4/4 etc. You think the coding should be like: 0/0 --> 1 Any other heterozygous combination [1/2, 0/1 etc] --> 2 All other homozygous combination [1/1, 3/3 etc] --> 3 But those positions are ignored when I run BioA ...
written 7 months ago by cannilay20
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Comment: C: SnpMatrix from VCF file
... What will you do in multiallelic cases? I have some GT values like 3/3, 1/2, 4/4 etc. You think the coding should be like: 0/0 --> 1 Any other heterozygous combination [1/2, 0/1 etc] --> 2 All other homozygous combination [1/1, 3/3 etc] --> 3 But those positions are ignored when I run your ...
written 7 months ago by cannilay20
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Answer: A: SnpMatrix from VCF file
... Hello! What will you do in multiallelic cases? I have some GT values like 3/3, 1/2, 4/4 etc. You think the coding should be like: - 0/0 --> 1 - Any other heterozygous combination [1/2, 0/1 etc] --> 2 - All other homozygous combination [1/1, 3/3 etc] --> 3 But those positions are ignor ...
written 7 months ago by cannilay20

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