Moderator: zx8754

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zx87549.0k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

<prev • 1,067 results • page 1 of 107 • next >
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Answer: A: Manhattan Plot in R with non-numeric CHR values
... We can cheat a little and make your chroms numeric, then use custom chrom labels, see this example: library(qqman) #example data from the package where CHR is numeric table(gwasResults$CHR) # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 ...
written 2 days ago by zx87549.0k
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Comment: C: QC after imputation
... Related post: - https://www.biostars.org/p/6476/ ...
written 4 days ago by zx87549.0k
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Comment: C: How to check for the presence/absence of unique rows in two different matrices?
... Something like: mySubset <- m1[ rownames(m1) %in% rownames(m2), ] ...
written 10 days ago by zx87549.0k
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Comment: C: How to label custom multiple gene lists object into volcano plot?
... Provide example input: *res* and *genes* objects. Note, there is a dedicated package for volcanoes - [EnhancedVolcano](https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html) ...
written 11 days ago by zx87549.0k
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Comment: C: Struggling to work on a large Count Matrix on Rstudio
... Do you mean "load/import" a big file? > charging my large count Matrix on R ...
written 11 days ago by zx87549.0k
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Comment: C: how to get gene symbol from Entrez id
... "nothing seems to be working" is not helpful, please provide the codes you have tried together with errors/warnings. ...
written 12 days ago by zx87549.0k
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Comment: C: how to get gene symbol from Entrez id
... Did you try searching? - https://www.biostars.org/p/69647/ - https://www.biostars.org/p/102375/ - https://www.biostars.org/p/255657/ - https://www.biostars.org/p/297745/ - https://www.biostars.org/p/394654/ ...
written 12 days ago by zx87549.0k
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Comment: C: Imputing specific SNPs using Beagle5.1
... Can't tell for sure, but I think impute2 has an option of only impute missing - "fill in", beagle should have something similar, too. If not another solution would be to trim down the panel to match your SNP list. ...
written 13 days ago by zx87549.0k
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Comment: C: Please interpret QUAST output.
... Please paste the output as text. ...
written 13 days ago by zx87549.0k
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Answer: A: R ggplot2 -
... Maybe facet by chromosomes: testDE <- read.table(text = "Gene_name Chr log2FoldChange padj significant row gene1 1 1.291089929 0.545016613 no 1 gene2 1 0.873801059 0.588763458 no 2 gene3 1 0.044171969 0.991428121 no 3 gene4 1 2.105103925 0.017808512 y ...
written 17 days ago by zx87549.0k

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