User: zhengx

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zhengx30
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New User
Location:
United States
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1 week, 1 day ago
Joined:
4 years, 1 month ago
Email:
z*****@u.washington.edu

Posts by zhengx

<prev • 17 results • page 1 of 2 • next >
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Answer: A: What does SNPRelate::snpgdsDiss calculate?
... See: Weir BS, Goudet J. A Unified Characterization of Population Structure and Relatedness. Genetics. 2017 Aug;206(4):2085-2103. doi: 10.1534/genetics.116.198424. `snpgdsDiss()` returns 1 - beta_ij. ...
written 8 days ago by zhengx30
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Answer: A: Different order of samples in output of snpgdsSlidingWindow to calculate Fst and
... SNPRelate re-orders "population" internally according to the order of sample IDs. res$sample.id is the sample order in the GDS file. If you are not sure whether the order of population is correct, you could order your input sample IDs as the order in the GDS file and provide population information ...
written 5 weeks ago by zhengx30
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Answer: A: SeqArray problem in seqVCF2GDS and convert back to vcf
... SeqArray_1.22.6 fixes the bug in the merged GDS file: merged <- seqOpen("merged.gds") seqAsVCF(merged) "Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: range cannot be determined from the supplied arguments (too many NAs)" ...
written 3 months ago by zhengx30
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Answer: A: SNPrelate, snpgdsFst is excluding all snps on non-autosomes, how can I get it to
... Try: snpgdsFst(genofile, sample.id = samp.sel, population = as.factor(pop.sel), method = "W&C84", autosome.only=FALSE)   ...
written 8 months ago by zhengx30
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Answer: A: Unable to build GDS with more than 255 scaffolds?
... Please use cvt.chr="char" in snpgdsBED2GDS(). See: ?SNPRelate::snpgdsBED2GDS​ ...
written 9 months ago by zhengx30
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Answer: A: Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems w
... Please make sure your file exists. You might try file.size(vcf.fn) to see whether it returns the correct size of that VCF file.   ...
written 10 months ago by zhengx30
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Comment: C: Avoid 'dStr8' format in the GDS files
... Please downgrade the gdsfmt package. snpgdsCreateGeno() has no option to control the type of characters. ...
written 14 months ago by zhengx30
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Answer: A: Write gds in parallel
... The answer is simple: I have not implemented GDS writing with multiple processes at the same time so far. We usually create multiple independent GDS files, and each process writes data to each separate GDS file. After all child processes are done, multiple GDS files are merged in the main process. ...
written 14 months ago by zhengx30
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Answer: A: Error converting vcf to gds
... You might try SeqArray::seqVCF2GDS(), which could provide you more error information.   ...
written 15 months ago by zhengx30
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Answer: A: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
... It seems I should use .onLoad instead of .onAttach.   ...
written 18 months ago by zhengx30

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