Man pages for bcm-uga/pcadapt
Fast Principal Component Analysis for Outlier Detection

assign.int.labelsConvert string labels to integer labels
bedadapt-classClass bedadapt
BED_rsvdSVD for genotype matrices stored in .bed files with missing...
cart2bary_cppCartesian coordinates to barycentric coordinates
clumpingLD clumping
cmpt_cov_cppCovariance for loaded genotype data
cmpt_global_pcaGlobal Principal Component Analysis
cmpt_loadingsCompute the loadings
cmpt_local_pcaLocal Principal Component Analysis
cmpt_minor_afMinor allele frequencies
cmpt.statpcadapt statistics
covRob_cppRobust estimates for location and scatter
create.pcadaptpcadapt objects
display.local.pcaLocal Ancestry
get_nb_indNumber of individuals in a specific population
get.output.nameReplace the file extension with the .pcadapt extension
get.pcGet the principal component the most associated with a...
get.pool.matrixConvert genotypes to pooled samples
get.pop.namesRetrieve population names
get_pop_sizeGet population size
get.score.colorPopulation colorization
get_size_cppFile size
get_window'get_window'
impute_genoGenotype matrix imputation
impute_geno_popGenotype matrix imputation
impute.pcadaptGenotype matrix imputation
lfmm2pcadaptConvert lfmm files
loc.anc.plottingLocal Ancestry
lrfunc_cppLinear regression
manhattan.plottingManhattan Plot
matrix_rsvdSVD for genotype matrices
neutral.plottingNeutral Distribution Estimation
pcadaptPrincipal Component Analysis for outlier detection
pca_rotation'pca_rotation'
ped2pcadaptConvert ped files
plot.pcadaptpcadapt visualization tool
print_convertSummary
pvalqq.plottingp-values Q-Q Plot
rdadaptRedundant Analysis for outlier detection
read.pcadaptFile Converter
residuals_to_statResiduals-based statistics
run.pcadaptShiny app
sample_geno_fileSample genotype matrix from pooled samples
sample_geno_matrixSample genotype matrix from pooled samples
scale_genoScale genotype matrices
scan.introIntrogression
score.plottingPrincipal Components Analysis Scores Plot
scree.plottingPrincipal Components Analysis Scree Plot
slidingWindows_fastIntrogression statistics
slidingWindows_newIntrogression statistics
svd.pcadaptSingular Value Decomposition
updt_local_scoresUpdate local Principal Component Analysis
vcf2pcadaptvcfR-based converter
vcf_convertConvert vcfR genotype matrices
bcm-uga/pcadapt documentation built on Nov. 7, 2017, 8:16 a.m.