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bigsnpr 1.6.5

  • Add parameter thr_r2 in snp_cor().

bigsnpr 1.6.4

  • Remove penalization in snp_ldsplit(). Instead, report the best splits for a range of numbers of blocks desired.

bigsnpr 1.6.3

  • Penalization in snp_ldsplit() now makes more sense. Also fix a small bug that prevented splitting the last block in some cases.

bigsnpr 1.6.2

  • Add function snp_ldsplit() for optimally splitting variants in nearly independent blocks of LD.

bigsnpr 1.6.1

  • Add option file.type = "--gzvcf" for using gzipped VCF in snp_plinkQC().

bigsnpr 1.6.0

  • Finally remove function snp_assocBGEN(); prefer reading small parts with snp_readBGEN() as a temporary bigSNP object and do the association test with e.g. big_univLinReg().

bigsnpr 1.5.7

  • Add function snp_thr_correct() for correcting for winner's curse in summary statistics when using p-value thresholding.

bigsnpr 1.5.6

  • Use a better formula for the scale in LDpred2, useful when there are some variants with very large effects (e.g. explaining more than 10% phenotypic variance).

  • Simplify LDpred2; there was not really any need for initialization and ordering of the Gibbs sampler.

bigsnpr 1.5.5

  • Add option return_sampling_betas in snp_ldpred2_grid() to return all sampling betas (after burn-in), which is useful for assessing the uncertainty of the PRS at the individual level (see https://doi.org/10.1101/2020.11.30.403188).

bigsparser 0.4.1

  • Faster cross-product with SFBM, which should make all LDpred2 models faster.

bigsnpr 1.5.4

  • Also return $postp_est, $h2_init and $p_init in LDpred2-auto.

bigsnpr 1.5.1

  • Add multiple checks in snp_readBGEN() to make sure of the expected format.

bigsnpr 1.5.0

  • Add function snp_fst() for computing Fst.

bigsnpr 1.4.11

  • Workaround for error could not find function "ldpred2_gibbs_auto".

bigsnpr 1.4.9 & bigsparser 0.4.0

  • Can now directly do as_SFBM(corr0) instead of bigsparser::as_SFBM(as(corr0, "dgCMatrix")). This should also use less memory and be faster.

bigsnpr 1.4.8

  • Add option sparse to enable getting also a sparse solution in LDpred2-auto.

bigsparser 0.3.0

  • Faster bigsparser::as_SFBM().

bigsnpr 1.4.7

  • Allow for format 01 or 1 for chromosomes in BGI files.

bigsnpr 1.4.6

  • Fasten snp_match(). Also now remove duplicates by default.

bigsnpr 1.4.3

  • Fix a bug when using very large correlation matrices in LDpred2 (although we do not recommend to do so).

bigsnpr 1.4.2

  • All 3 LDpred2 functions now use an SFBM as input format for the correlation matrix.

  • Allow for multiple initial values for p in snp_ldpred2_auto().

  • Add function coef_to_liab() for e.g. converting heritability to the liability scale.

bigsnpr 1.4.1

  • Change default of parameter alpha of function snp_cor() to 1.

bigsnpr 1.4.0

  • Add functions snp_ldpred2_inf(), snp_ldpred2_grid() and snp_ldpred2_auto() for running the new LDpred2-inf, LDpred2-grid and LDpred2-auto.

  • Add functions snp_ldsc() and snp_ldsc2() for performing LD score regression.

  • Add function snp_asGeneticPos() for transforming physical positions to genetic positions.

  • Add function snp_simuPheno() for simulating phenotypes.

bigsnpr 1.3.1

  • Also use OpenMP for the parallelization of snp_pcadapt(), bed_pcadapt(), snp_readBGEN() and snp_fastImputeSimple().

bigsnpr 1.3.0

  • Parallelization of clumping algorithms has been modified. Before, chromosomes were imputed in parallel. Now, chromosomes are processed sequentially, but computations within each chromosome are performed in parallel thanks to OpenMP. This should prevent major slowdowns for very large samples sizes (due to swapping).

  • Use OpenMP to parallelize other functions as well (possibly only sequential until now).

bigsnpr 1.2.6

  • Can now run snp_cor() in parallel.

  • Parallelization of snp_fastImpute() has been modified. Before this version, chromosomes were imputed in parallel. Now, chromosomes are processed sequentially, but computation of correlation between variants and XGBoost models are performed using parallelization.

bigsnpr 1.2.5

  • Add function snp_subset() as alias of method subset() for subsetting bigSNP objects.

bigsnpr 1.2.4

  • Use new class bed_light internally to make parallel algorithms faster because they have to transfer less data to clusters. Also define differently functions used in big_parallelize() for the same reason.

bigsnpr 1.2.0

  • Use the new implementation of robust OGK Mahalanobis distance in {bigutilsr}.

bigsnpr 1.1.1

  • Fix error object 'obj.bed' not found in snp_readBed2().

bigsnpr 1.1.0

  • Cope with new read-only option in {bigstatsr} version >= 1.1.

bigsnpr 1.0.2

  • Add option backingfile to subset.bigSNP().

bigsnpr 1.0.1

  • Add option byrow to bed_counts().

bigsnpr 1.0.0

  • Add memory-mapping on PLINK (.bed) files with missing values + new functions:

    • bed()
    • bed_MAF()
    • bed_autoSVD()
    • bed_clumping()
    • bed_counts()
    • bed_cprodVec()
    • bed_pcadapt()
    • bed_prodVec()
    • bed_projectPCA()
    • bed_projectSelfPCA()
    • bed_randomSVD()
    • bed_scaleBinom()
    • bed_tcrossprodSelf()
    • download_1000G()
    • snp_modifyBuild()
    • snp_plinkKINGQC()
    • snp_readBed2()
    • sub_bed()

  • Add 3 parameters to autoSVD(): alpha.tukey, min.mac and max.iter.

  • Remove option for changing ploidy (that was only partially supported).

  • Automatically apply snp_gc() to pcadapt.

bigsnpr 0.12.0

  • Add snp_fastImputeSimple(): fast imputation via mode, mean or sampling according to allele frequencies.

bigsnpr 0.11.3

  • Fix a bug in snp_readBGEN() that could not handle duplicated variants or individuals.

bigsnpr 0.11.1

  • When using snp_grid_PRS(), it now stores not only the FBM, but also the input parameters as attributes (the whole result basically).

bigsnpr 0.11.0

  • Add 3 SCT functions snp_grid_*() to improve from Clumping and Thresholding (preprint coming soon).

  • Add snp_match() function to match between summary statistics and some SNP information.

bigsnpr 0.10.2

  • Parameter is.size.in.bp is deprecated.

bigsnpr 0.10.1

  • Add parameter read_as for snp_readBGEN(). It is now possible to sample BGEN probabilities as random hard calls using read_as = "random". Default remains reading probabilities as dosages.

bigsnpr 0.10.0

  • For memory-mapping, now use mio instead of boost.

  • snp_clumping() (and snp_autoSVD()) now has a size that is inversely proportional to thr.r2.

  • snp_pruning() is deprecated (and will be removed someday); now always use snp_clumping().

bigsnpr 0.9.0

  • When reading bed files, switch reading of Os and 2s to be consistent with other software.

bigsnpr 0.8.2

  • Add function snp_assocBGEN() for computing quick association tests from BGEN files. Could be useful for quick screening of useful SNPs to read in bigSNP format. This function might be improved in the future.

bigsnpr 0.8.1

  • Change url to download PLINK 1.9.

bigsnpr 0.8.0

  • Add function snp_readBGEN() to read UK Biobank BGEN files in bigSNP format.

bigsnpr 0.7.0

  • Add parameter is.size.in.bp to snp_autoSVD() for the clumping part.

  • Change the threshold of outlier detection in snp_autoSVD() (it now detects less outliers). See the documentation details if you don't have any information about SNPs.

bigsnpr 0.6

  • Keep up with {bigstatsr}.

bigsnpr 0.3.1

  • Provide function snp_gene (as a gist) to get genes corresponding to 'rs' SNP IDs thanks to package {rsnps} from rOpenSci. See README.

bigsnpr 0.3.0

bigsnpr 0.2.7

  • Faster defaults + possibility to estimate correlations based on a subset of individuals for snp_fastImpute. Also store information in an FBM (instead of a data frame) so that imputation can be done by parts (you can stop the imputation by killing the R processes and come back to it later). Note that the defaults used in the Bioinformatics paper were alpha = 0.02 and size = 500 (instead of 1e-4 and 200 now, respectively). These new defaults are more stringent on the SNPs that are used, which makes the imputation faster (30 min instead of 42-48 min), without impacting accuracy (still 4.7-4.8% of errors).

bigsnpr 0.2.5

  • This package won't be on CRAN.

bigsnpr 0.2.4

  • No longer download PLINK automatically (because it is a CRAN policy violation).