Moderator: zx8754

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zx87549.7k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

<prev • 1,162 results • page 1 of 117 • next >
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Comment: C: Merge overlapping and adjacent features in the BED file having the same label in
... Split by "label" then reduce. ...
written 5 days ago by zx87549.7k
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Comment: C: Linkage disequilibrium, plot, package, script, rstudio.
... There are many packages for plotting LD, e.g.: [LDheatmap](https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf) ...
written 9 days ago by zx87549.7k
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Comment: C: Linear Model Loop in R
... Try: res <- Data[ paste0(i,".res") ] pred <- Data[ paste0(i,".pred") ] ...
written 11 days ago by zx87549.7k
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Comment: C: Subsetting a data by a regions from BED file
... Search for "merge by range overlap", related SO post: https://stackoverflow.com/q/24480031/680068 And see my example answer here: https://www.biostars.org/p/339679/#339699 ...
written 19 days ago by zx87549.7k
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Comment: C: Post GWAS mapping SNPs to genes and calculating p-values
... There are many many posts already, please search for "snp to gene", "snp annotation", "positions to genes", etc - https://www.biostars.org/p/18522/ - https://www.biostars.org/p/413/ - https://www.biostars.org/p/110254/ - https://www.biostars.org/p/111225/ - https://www.biostars.org/p/142/ - h ...
written 23 days ago by zx87549.7k
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Comment: C: Likelihood distance matrix ( .mldist) to .csv or .txt
... Cross-posted at SO: https://stackoverflow.com/q/64682309/680068 ...
written 24 days ago by zx87549.7k
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Comment: C: Attempt to set 'rownames' on an object with no dimensions
... If this resolved your issue accept as answer - tick. ...
written 26 days ago by zx87549.7k
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Answer: A: Issues with identifying chromosomes for a list of SNPs
... Usign *biomaRt*: #set up library(biomaRt) snpmart = useEnsembl(biomart = "snp", dataset="hsapiens_snp") #Other useful functions # listAttributes(snpmart) # listFilters(snpmart) Get SNPs that match with our list of IDs, here we have 2 SNP from chr1 and 1 SNPs from chr2: ...
written 26 days ago by zx87549.7k
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Comment: C: manhattan plot for different color in R
... No, "green" is hardcoded. You could copy the code from GitHub and change it to any colour, see [GitHub manhattan.R#L211](https://github.com/stephenturner/qqman/blob/master/R/manhattan.R#L211) ...
written 26 days ago by zx87549.7k
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Answer: A: manhattan plot for different color in R
... We could use *highlight* argument, try this example: library(qqman) #dummy data from qqman d <- gwasResults #add groups set.seed(1); d$grp <- sample(1:2, nrow(d), replace = TRUE) manhattan(d, col = "red", highlight = d[ d$grp == 2, "SNP"]) ...
written 26 days ago by zx87549.7k

Latest awards to zx8754

Scholar 13 days ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 5 weeks ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Scholar 8 weeks ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 9 weeks ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 10 weeks ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Scholar 3 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 3 months ago, created an answer that has been accepted. For A: How to name column header for first column ?
Scholar 3 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 3 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 4 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 5 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Scholar 5 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Scholar 5 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Asking The Developers Before Asking Biostars
Scholar 9 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?

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