SNPRelate

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snpgdsCombineGeno makes new snp.id when combine multiple gds files

2

I have several gds files. Their snp.id are numeric but not continuous. Gds file 1 has snp.id like 1, 2, 3, ...,10; Gds file 2 has 20, 21, ...., 30....

yangli-ai

Hi! Could you please let me know how can I possibly modify the Y-axis of individual dissimilarity? I do not know why is it much shorter can the coancestry coefficient....

Carol-Symbiomics

mergi-2674

Hi, I used the `snpgdsFst` function to calculate the Fst values, and it returned the mean and weighted Fst values. Could someone please tell me the meaning of the weighted...

NamLQ

family information in snpgdsGDS2PED

2

How can I translate my .gds into .ped and automatically taking the family information from my gds object which I added before with add.gdsn() ? Such as from: + [...

treebreeder

snpgdsLDpruning result to gds/vcf

7

Dear developer(s), I wonder if there is any chance to get a gds (or vcf) file once a snp dataset (with multiple samples inside) has been pruned. Unfortunately I am...

linsson

snpgdsSlidingWindow winstart= bug

3

Dear @zhengxwen, I am running v1.20.1 of SNPRelate and tried to find out the start / end coordinates of the sliding windows I computed with snpgdsSlidingWindow(). I realized that when...

marqueda

Ids in plink bed are not unique

2

Hello, I am using SNPRelate to investigate my variants. When I run: `snpgdsBED2GDS(bed_r1321,bim_r1321,fam_r1321,'r1321.gds',cvt.snpid = 'auto')` I am getting this: ``` Start file conversion from PLINK BED to SNP GDS ......

zillurbmb51

alleles switch in snpgdsBED2GDS ?

10

Hi, According to the doc of snpgdsCreateGeno: snp.allele{the reference/non-reference alleles} and in snpgdsBED2GDS, line 298: ``` bimD

kforner

LDpruning really using num.threads?

2

I've set this parameter on the snpgdsLDpruning() function and I even get back Working space: 316 samples, 795,668 SNPs using 24 (CPU) cores however every time I look at cpu...

rafalcode