Man pages for hemstrow/snpR
Whole-genome analysis tools for use with SNP data.

add.facets.snpR.dataAdd facets to snpRdata objects
apply.snpR.facetsApply functions across snpR facets.
calc_associationRun case/control association tests on SNP data.
calc_basic_snp_statsCaluclate basic SNP statistics
calc_pairwise_ldPairwise LD from SNP data.
calc_p_from_bootstrapsCaculate p-values from bootstrapped distributions.
calc_single_statsCalculate standard single-SNP genetic statistics
calc_smoothed_averagesGaussian smooth statistics across sliding windows.
calc_tajimas_dTajima's D from SNP data.
call_colonyCall a prepared colony infile.
check_duplicatesChecks for duplicated samples in snpRdata.
check.snpR.facet.requestGet details on and clean up facet arguments.
cross_validate_genomic_predictionRun a single cross-validation with BGLR.
do_bootstrapsGenerate bootstrapped windowed statistics
Facets_in_snpRFacets in snpR
filter_snpsFilter SNPs in snpRdata objects.
find.snpR.facetsGrab information of the facets present in snpRdata objects.
format_snpsRe-format SNP data.
gaussian_weightCalculate gaussian weights.
get.snpR.statsPull calculated statistics from snpRdata objects.
import.snpR.dataImport genotype and metadata into a snpRdata object.
interpolate_snInterpolate sn formatted data.
merge.snpR.statsMerge newly calculated stats into a snpRdata object.
parse_colonyParse colony data.
plot_clustersPCA and tSNE plots from snpRdata.
plot_pairwise_LD_heatmapCreate a heatmap from pairwise linkage data.
run_colonyCreate and infile, run, and gather some basic results using...
run_genomic_predictionInterface with BGLR to run genomic prediction with snpRdata...
sanity_check_windowDo sanity checks for many window specific functions in snpR.
snpRdata-classStorage class for snpR data and calculated statistics.
stickFORMATsList containing example data in all formats exportable by...
stickRAWDeschutes stickleback raw data.
stickSNPsDeschutes stickleback example snpRdata.
subset_snpR_dataSubset snpRdata objects
tabulate_genotypesTabulate allele and genotype counts at each locus.
write_colony_inputWrite an input for the COLONY pedigree assignment program.
hemstrow/snpR documentation built on July 11, 2019, 8:44 p.m.