Date Version Changes
02-21-2018 4.0 - read.pcadapt generates bed files instead of pcadapt files.
- Computation of PCA is based on the package RSpectra.
- Missing values are handled by specifying vector-matrix operation in RSpectra that accounts for missing values.
- Includes LD thinning to compute PCs.
- No more dependency to RcppArmadillo
- For Pooled-seq data, use Mahalanobis distances based on PCA loadings, no more simulations of individuals genotypes
01-15-2017 3.1.0 - Switch from C/Lapack to Rcpp/RcppArmadillo.
- pcadapt can take genotype matrices as input.
- Modified code for binomial sampling.
- pcadapt argument clean.files is now deprecated.
- pcadapt argument output.filename is now deprecated.
- read.pcadapt argument local.env is now deprecated.
- Latest update of vcfR taken into account.
12-20-2016 3.0.4 - Method based on sampling genotypes added to handle pooled-sequencing.
10-06-2016 3.0.3 - Option type="vcfR" has been added to read.pcadapt to overcome some conversion issues occurring with VCF files.
- Argument transpose is now deprecated. Read section A for more details.
06-13-2016 3.0.2 - The function get.pc has been added. For each SNP, it returns the most correlated principal component.
06-01-2016 3.0.1 - The read4pcadapt is now deprecated, it is now called read.pcadapt.
- Using the pop option when plotting scores now provides the color legend.
04-04-2016 3.0 - All analyses are now included in the R package. Users should not use the C software PCAdapt fast anymore.
- Big datasets can be handled directly within the R session.
- read4pcadapt now converts files to the pcadapt format.
- The first argument of pcadapt can be either a small genotype matrix or the output of read4pcadapt.
02-12-2016 2.2 - The Mahalanobis distance is now estimated from the z-scores rather than the loadings.
12-18-2015 2.1 - The scaling of the SNP before computing PCA has been changed. Instead of using standard deviation, we now use the square root of $$p(1-p)$$ (haploid data) or of $$2p(1-p)$$ (diploid data) where $$p$$ is the minimum allele frequency.
- Bug fix: the genomic inflation factor has been corrected when K=1.
- Argument "minmaf" has been replaced with "min.maf".
2.0.1 - Vignette corrected: when reading output from the software PCAdapt, we do not mention the deprecated argument PCAdapt in the function pcadapt.