Moderator: zx8754

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zx87549.4k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

<prev • 1,120 results • page 2 of 112 • next >
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Answer: A: Error in plot_AS_segfit
... Error message is clear, we have no values in `loci.annot`, see this example: loci.annot <- character() length(loci.annot) # [1] 0 !is.na(character()) # logical(0) if( !is.na(character()) ) { "yes" } else { "no" } # Error in if (!is.na(character())) { : argu ...
written 27 days ago by zx87549.4k
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Comment: C: Converting Variant ID to RsID in batch
... Convert the IDs to `chr, pos, a1, a2`, then see these posts: - https://www.biostars.org/p/64105/ - https://www.biostars.org/p/72066/ - https://www.biostars.org/p/312369/ ...
written 4 weeks ago by zx87549.4k
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Comment: C: Reordering legend labels and changing arrow length in Enhanced Volcano
... Provide example data, and your current code. ...
written 4 weeks ago by zx87549.4k
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Comment: C: Problems with package installation in R studio 4.0.2
... Hello psong5757! We believe that this post does not fit the main topic of this site. Not related to bioinformatics. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a repl ...
written 4 weeks ago by zx87549.4k
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Answer: A: PED file PLINK
... It is [Irregularly-formatted PLINK text files](https://www.cog-genomics.org/plink/1.9/input), using below flags that ped file should work fine: plink --file myFile --no-fid --no-parents --no-sex --no-pheno --make-bed --out myFileBinary ...
written 5 weeks ago by zx87549.4k
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Comment: C: Exporting files from Plink with sample IDs?
... Since you are using `--tfile` flag, then you must have *examplesnps.tped* and *examplesnps.tfam* (which has the same format as [.fam file](https://www.cog-genomics.org/plink/1.9/formats#fam)). That tfam file would have the sample IDs. ...
written 5 weeks ago by zx87549.4k
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Comment: C: GSEA for genes in R
... Maybe just make your own set of genes? Doesn't have to a be a pathway. There are many R packages, here is one from Bioconductor: - https://bioconductor.org/packages/release/bioc/html/GSEABase.html ...
written 5 weeks ago by zx87549.4k
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Answer: A: How to combine two networks
... Using **R** igraph union: library(igraph) net1 <- graph_from_literal(A-B:C:D, A-C, B-C) net2 <- graph_from_literal(A-X:Y:Z, Z-Y) par(mfrow = c(1, 3)) set.seed(1) plot(net1, vertex.size = 50, main = "net1") plot(net2, vertex.size = 50, main = "net2") p ...
written 6 weeks ago by zx87549.4k
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Comment: C: Change the field separator
... Maybe read the manual for **sed**? https://en.wikipedia.org/wiki/Sed ...
written 6 weeks ago by zx87549.4k
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Answer: A: Change the field separator
... Using **R**, just read the file with *sep*: read.table("myFile.txt", sep = "/") # V1 V2 V3 V4 V5 V6 V7 V8 #1 CG10226 CG33120 RyR Tsp42Eg CG1234 Act57B Apoltp CG9194 ...
written 6 weeks ago by zx87549.4k

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Scholar 5 weeks ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
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