User: Qiang

gravatar for Qiang
Qiang30
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1 month, 1 week ago
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3 years, 4 months ago
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q*******@roswellpark.org

Posts by Qiang

<prev • 7 results • page 1 of 1 • next >
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Comment: C: The metadata from rowRanges is missing in the MAP function of GenomicFiles.
... The workaround works. Thanks! ...
written 7 weeks ago by Qiang30
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The metadata from rowRanges is missing in the MAP function of GenomicFiles.
... Hi all, I want to pass metadata **ref** in `rowRanges` to the MAP function when using `reduceByFile` from GenomicFiles. ``` fls <- tempfile() gr <- GRanges("chr1", IRanges(c(1, 10), width = 10)) gr$ref <- c("a", "b") gf <- GenomicFiles(files=fls, rowRanges=gr) MAP <- function(range ...
genomicfiles written 7 weeks ago by Qiang30 • updated 7 weeks ago by Martin Morgan ♦♦ 23k
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Comment: C: ranges input for GenomicFiles
... Thank you for your reply. Because my input require extra data for each range. I guess I could extend a `GRanges` class with extra `elementMetadata` as input for my function, but convert it back to `GRanges` when using `reduceBy` functions. ...
written 17 months ago by Qiang30 • updated 17 months ago by Martin Morgan ♦♦ 23k
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ranges input for GenomicFiles
... Hi, I am working on a function with VCF/variants and BAM as input. The reduceByFile/reduceByRange are imported in my function, which require GRanges/GRangesList as ranges input. However, my input requires a extented GRanges class with variants(DNAStringSet) in elementMetadata, like, CollapsedVCF. I ...
genomicfiles written 18 months ago by Qiang30 • updated 17 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Error in parseURI("") : cannot parse URI (rtracklayer package)
... The problem is solved after updating libxml2 to 2.9.1. Thanks! ...
written 3.3 years ago by Qiang30
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Comment: C: Error in parseURI("") : cannot parse URI (rtracklayer package)
... Both have the same XML_3.98-1.4 installed, but the libxml2 version are different. The problem one: /usr/lib/libxml2.so -> libxml2.so.2.6.26 The working one: /usr/lib/x86_64-linux-gnu/libxml2.so -> libxml2.so.2.9.1 Do I have to upgrade the libxml2 to 2.9? I don't have permission to do that ...
written 3.3 years ago by Qiang30
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Error in parseURI("") : cannot parse URI (rtracklayer package)
... Hi Lawrence, I got an error when testing the import function. track <- import(system.file("tests", "v1.gff", package = "rtracklayer")) Error in parseURI("") : cannot parse URI I found the parseURI("") was used in the .parseURI function when it run in unix system (io.R line 200). parsed < ...
rtracklayer written 3.3 years ago by Qiang30

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