User: zhengx

gravatar for zhengx
zhengx20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
3 weeks, 1 day ago
Joined:
3 years, 10 months ago
Email:
z*****@u.washington.edu

Posts by zhengx

<prev • 15 results • page 1 of 2 • next >
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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 weeks ago by zhengx20
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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 6 months ago by zhengx20
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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 7 months ago by zhengx20
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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 8 months ago by zhengx20
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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 11 months ago by zhengx20
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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 11 months ago by zhengx20
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Answer: A: Error converting vcf to gds
... You might try SeqArray::seqVCF2GDS(), which could provide you more error information.   ...
written 12 months ago by zhengx20
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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 16 months ago by zhengx20
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Answer: A: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
... You should explicitly import the namespace of SeqArray. please use library(SeqArray) or require(SeqArray)     ...
written 16 months ago by zhengx20
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Answer: A: Cannot read plink files correctly
... Start snpgdsBED2GDS ...     BED file: "lebanon_complete.bed" in the SNP-major mode (Sample X SNP)     FAM file: "lebanon_complete.bim", DONE.     BIM file: "lebanon_complete.fam", DONE. You have used the wrong FAM and BIM files.   ...
written 22 months ago by zhengx20

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