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Dear Han,
Sorry for disturbing you sir. Could you please help me decipher why the GMMAT package package does not completely install on my Windows PC?. I am using the latest version of R and RSt…
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I try to convert a .vcf.gz file to tidy genomic data in Rstudio:
`eu_snps_1 file.exists("strata_eu.tsv")
[1] TRUE`
`> file.exists("UMBELLA_Erumb1_samples_gt_50pct_covered.recode.vcf.gz")
[1] T…
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Using the vcf file provided in the email, I get two problems using SeqArray::seqVCF2GDS differently:
**1. without parallel**
```
test
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When a VCF file is imported SeqArray reads and use the default ref/alt alleles.
However, when samples are removed, depending on MAC/MAF, ref/alt alleles might change ...
**Question**
Is there a q…
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Hi,
Running radiator, updated package and tested just a few minutes ago (and was getting it the past week on radiator 1.0.0), using R 3.5.1 on Windows.
I have been unable to convert a VCF output…
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Hi Xiuwen,
I have another VCF file generating an error with SeqArray. This time, the vcf file was produced with freeBayes v1.1.0-4-gb6041c6
Here's the command:
```
require(magrittr)
check %
…
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Hi Thierry,
Trying to import a vcf using tidy_genomic_data without filtering common markers, but it filters them anyway:
```
tidy.sphanorth124spatial.radiator.50pctmsng2
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Hi, this is actually the first time I encountered this issue after using SeqArray for few weeks without error. Here is the log:
```
> library(SeqArray)
> library(SNPRelate)
> library(GenomicRanges…
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Hi Thierry,
A few small bugs I've noticed with filter_rad() in interactive mode:
-Any filter that removes samples/individuals causes failure in the next filtering step:
```
Error: Column `MISS…
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Message:
Error in seqVCF2GDS(vcffile, gdsfile.tmp, fmt.import = fmt.import, storage.option = "LZMA_RA", :
Invalid integer conversion '1|1'
SessionInfo:
R version 3.5.1 (2018-07-02)
Platfo…