User: endrebak85

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endrebak8530
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github.com/endrebak/
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3 years, 5 months ago
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Posts by endrebak85

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Finding the proper universe for enrichGO and enrichKEGG - only the genes that ar
... library(org.Hs.eg.db) df = as.data.frame(org.Hs.egGO) go_gene_list = unique(sort(df$gene_id)) dfk = as.data.frame(org.Hs.egPATH) kegg_gene_list = unique(sort(dfk$gene_id)) ...
written 7 weeks ago by endrebak8530
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Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
... I want to find the correct background gene list ("universe") to use with ChIPseeker. Ideally I would like to use all the genes that are annotated in GO as the universe for enrichGO and all the genes that are annotated in KEGG for enrichKEGG. Does anyone know how to find these lists? The current way ...
chipseeker written 7 weeks ago by endrebak8530
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Comment: C: How do I do a bedtools like intersection in GenomicRanges?
... It is just pintersect, no? ...
written 15 months ago by endrebak8530
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Comment: C: How do I do a bedtools like intersection in GenomicRanges?
... Brilliant. Thanks! ...
written 15 months ago by endrebak8530
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Comment: C: nearest without overlapping
... Wouldn't the code be faster with precede(query, subject, select="first"), follow(query, subject, select="last") ? The only problem is that the code errors: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'from' for signature '"int ...
written 15 months ago by endrebak8530
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How do I do a bedtools like intersection in GenomicRanges?
... GenomicRanges intersect is more like what I would call set intersect - first the sets of A and B are computed, then intersection is done. Bedtools intersect finds the intersect of each interval in A with each interval in B which means that in the worst case, the number of output regions is the size ...
genomicranges written 15 months ago by endrebak8530 • updated 15 months ago by Michael Lawrence11k
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nearest without overlapping
... How I find distanceToNearest without overlapping ranges? I cannot see a flag for it in the docs. Any plans to add this? ...
genomicranges written 15 months ago by endrebak8530 • updated 15 months ago by Hervé Pagès ♦♦ 14k
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Avoid rotating vector when doing arithmetic on different length IRanges RleList entries
... I want to deduct the coverage in one RleList from that of another. A - B. But the lengths of the coverages aren't going to be exactly the same, which means that the vectors will be rotated. This is not what I want. For example, if the Rle in chr1 in A is longer than that in B I want to extend chr1 ...
iranges s4vectors rle rlelist written 15 months ago by endrebak8530
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Comment: C: csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
... Brilliant, I'll wager this is it. Thanks. ...
written 2.1 years ago by endrebak8530
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csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
... csaw version: csaw_1.10.0 The call to combineTests below fails: > tabcom <- combineTests(merged$id, results$table) Error: length(ids) == nrow(tab) is not TRUE > length(merged$id) [1] 14051634 > nrow(results$table) [1] 120695 When I get this error, what might the possible causes be? ...
csaw written 2.1 years ago by endrebak8530 • updated 2.1 years ago by Aaron Lun25k

Latest awards to endrebak85

Great Question 15 months ago, created a question with more than 5,000 views. For How do I merge a list of GRanges?
Popular Question 15 months ago, created a question with more than 1,000 views. For How do I merge a list of GRanges?
Popular Question 20 months ago, created a question with more than 1,000 views. For How do I merge a list of GRanges?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For How do I merge a list of GRanges?
Supporter 2.6 years ago, voted at least 25 times.
Scholar 2.7 years ago, created an answer that has been accepted. For A: edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign functio

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