Moderator: zx8754

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zx87546.2k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

<prev • 709 results • page 1 of 71 • next >
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Comment: C: GWAS Make bed file from fam and bim and Polygenic Risk Score calculation
... I don't understand the question. Please clarify. If this is about [Plink formats](https://www.cog-genomics.org/plink/1.9/), then: - **bim** is a map file for variants, like chr, pos... - **fam** is a phenotype file, FID, IID, sex, status... - **bed** is a binary genotype file, which is completely u ...
written 16 hours ago by zx87546.2k
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Comment: C: R RGL plot3d different symbols
... Did you try using the `pch` argument? Instead of assigning one value (`19`), try to map your groupings? ...
written 1 day ago by zx87546.2k
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Comment: C: how to get R squared value in scatter plot in cummeRbund
... Looks like plots are created using ggplot2, maybe use `myPlot + annotate("text", ...)`, see the manual: - [Create an annotation layer](https://ggplot2.tidyverse.org/reference/annotate.html) ...
written 1 day ago by zx87546.2k
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Comment: C: PLINK meta-analysis when there is SNP for just one study
... I am **guessing**, if we do not use `report-all`, that SNP won't be present in the output file. With `report-all` option we are saying list the SNP even if there is no stat, hence NA. I prefer [METAL](https://genome.sph.umich.edu/wiki/METAL_Quick_Start) for meta analysis, which reports for all SNPs ...
written 4 days ago by zx87546.2k
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Comment: C: Add `chr` to first column of specific rows?
... Could be done using R, but this is more suitable to command line, sed, awk,... ...
written 6 days ago by zx87546.2k
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Comment: A: Error in if (more || nchar(output) > 80) { : missing value where TRUE/FALSE n
... Also posted at SO: - https://stackoverflow.com/q/54106078/680068 ...
written 6 days ago by zx87546.2k
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Comment: C: about plot interaction network diagram in R
... See this tutorial by Katya Ognyanova. It is one of the most comprehensive ones with lots of examples: - [Static and dynamic network visualization with R](http://kateto.net/network-visualization) ...
written 7 days ago by zx87546.2k
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Comment: C: Plotting F3 statistics values on world map
... Provide example data. ...
written 29 days ago by zx87546.2k
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Comment: C: Allele frequency visualization
... This question is too broad, let us know what you have in mind. Can you share links to some papers that have the plots you liked? ...
written 29 days ago by zx87546.2k
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Comment: C: Drug interaction not running in MAFtools
... This looks like being handled by the author at [GitHub issue 212](https://github.com/PoisonAlien/maftools/issues/212) ...
written 29 days ago by zx87546.2k

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