SNPRelate
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zhengxwen
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
Hello, I sometimes experiment deadlocks using SNPRelate::snpgdsIBS with multiple threads. It is in one of my tests, and I have to run my whole testsuite multiple times to be able...
Does snpgdsBED2GDS do any conversion of the chromosome codes in the PLINK file? PLINK has 24=Y and 25=XY, while GWASTools assumes 24=XY and 25=Y. Could you add this option if...
Thanks for the package. I'm running v.1.16.0 (the latest my current version of R will allow), and am having some issues loading in multiple files. I think I am simply...
Hello, I am running SNPrelate on my genlight file from DART, and converting it to a gds. Using the code bellow, I get an error at the SNP pruning step....
I am using SNPRelate to produce a distance-based tree starting from a vcf file containing SNPs produced with ddRADseq. I was curious to know which agglomerative method was employed in...
Hi , I wonder whether there is a separation function for conducting the matrix-vector multiplication directly like prodvec or cross-product function, https://privefl.github.io/bigsnpr/reference/bed_cprodVec.html. It looks like such multiplication has been implemented...
Hi, I tried to use snpgdsLDpruning() for the first time, but I get a pruned snp dataset with no SNPs. This is the code I used: My dataset comes for...
Hello, I am really struggling to get individual weights of SNPs from a pca analysis. I can get the weights from each individual, but I would really like to get...
Dear Dr Zheng, I am trying to add a node to my GDA file, but I am struggling a lot with it, so I would love some advice and help...
I am having the error during installation. not sure what I am missing since I am using the BiocManager > if (!requireNamespace("BiocManager", quietly=TRUE)) + install.packages("BiocManager") > BiocManager::install("gdsfmt") 'getOption("repos")' replaces Bioconductor...
