User: Denis

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Denis30
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Posts by Denis

<prev • 56 results • page 1 of 6 • next >
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... Hi! `cat` is linux shell command. Please check: [http://www.linfo.org/cat.html][1] [1]: http://www.linfo.org/cat.html ...
written 4 days ago by Denis30
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Comment: C: Fast LD computation from VCF files using tomahawk
... `include.lowest = T` helped me a lot, otherwise i would get: Warning message: Removed 3029 rows containing missing values (geom_point). So i used the code: ld$r2c <- cut(ld$R2,breaks=seq(0,1,0.2),include.lowest = T,labels=c("0-0 - 0.2","0.2 - 0.4", ...
written 4 weeks ago by Denis30
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Making nice plots based on the different metrics from VCF file
... Hi all, I have a multi sample `VCF` file and i'd like to make a numerous plots with different metrics of the mentioned file for some report/presentation. I use `bcftools` for that, but wondering if there are any other useful tools or `R` functions, etc. for my purposes? Thanks! ...
genome R snp written 5 weeks ago by Denis30 • updated 5 weeks ago by Pierre Lindenbaum116k
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Comment: C: Fast LD computation from VCF files using tomahawk
... Thanks a lot for the great tutorial. Let me a few questions about `plotPairwiseLD` function please? 1.Could you please provide links to the `get()`, `filter()` and `arrange()` functions documentation (or may be add a short explanations for them in comments)? 2. Why we extract only elemets with `POS_ ...
written 6 weeks ago by Denis30
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Interpretation of Tassel MLM output
... I've performermed `GWAS` by `MLM` in `Tassel` and got a tables with results. What is the meaning and biological interpretation of `Effect` and `MarkerR2` columns of tables below (short example): Table1 Trait Marker Locus Site Allele Effect Obs H S01_13979 1 13979 C -2,34E+01 57 H S01_13 ...
genome gwas snp written 9 weeks ago by Denis30
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Comment: C: PLINK Haplotype blocks estimation not working
... I've solved the issue by adding `--blocks no-pheno-req` to the plink 1.9 command line. ...
written 11 weeks ago by Denis30
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Calculate a square matrix of r2 between all SNPs in genome during LD analysis
... I have a multiple genotypes in `vcf` format. I'd like to calculate a square matrix of `r2` between each pair of SNPs in genome (even for these located in differen chromosomes). Below is a toy example i wish to get: rs1 rs2 rs3 rs1 1 0.8 0.3 rs2 0.8 1 0. ...
genome R snp written 11 weeks ago by Denis30
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... Thanks for sharing that! It helped me a lot! Let me a question please? 1) You created mid column in the command: dfr1 <- dfr1 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")), end=as.integer(str_extract(str_repl ...
written 11 weeks ago by Denis30
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi, i'm curious,if the `SNPRelate` will give bootstrap values along with a tree? If i'm correct i tried a `SNPhylo` several years ago, but was not able to get any tree. Recently i've converted `VCF` file to `Hapmap` and then by means of `R`/`Bash` scripting converted it to the `fasta` alignment even ...
written 12 weeks ago by Denis30
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... I'm looking for the similar software, but i need a tree with bootstrap supports. Do you know any ready solution? Tassel doesn't do that unfortunately. ...
written 12 weeks ago by Denis30

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