User: zhengx

gravatar for zhengx
zhengx30
Reputation:
30
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New User
Location:
United States
Last seen:
1 week, 3 days ago
Joined:
4 years, 2 months ago
Email:
z*****@u.washington.edu

Posts by zhengx

<prev • 18 results • page 1 of 2 • next >
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Answer: A: seqVCF2GDS Error Converting VCF to GDS file
... You can directly modify the header in R: hdr <- seqVCF_Header("data/72S1.vcf.gz") hdr$info$Number[hdr$info$ID == "GMAF"] <- "." gdsfile <- seqVCF2GDS(vcffile, gdsfile, header=hdr) ...
written 10 days ago by zhengx30
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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 9 weeks 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 3 months 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 5 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 10 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 11 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 12 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 15 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 15 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 17 months ago by zhengx30

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