Man pages for eriqande/genoscapeRtools
Tools for building migratory bird genoscapes
| apwnd_window_internal | Compute average pairwise nucleotide diversity statistics for... |
| apwnd_windows | break markers up into non-overlapping windows and compute... |
| compile_assayable | return SNPs and say whether the are assayable or not, along... |
| comp_pair | make a comparison between two groups that are in df |
| convert_012_to_bed | create a PLINK bed file from and 012 matrix |
| correct_ass_prob | from vectors of snp allele freqs, compute the expected prob... |
| geno_freq_calcs | from on 012 file compute expected and observed genotype... |
| geno_freq_calc_single | from on 012 file compute expected and observed genotype... |
| genoscape_pca | do a PCA using SNPRelate and prepare output for rapid... |
| genoscapeRtools | My package documentation … bla bla … |
| ggplot_the_Qs | ggplot the Qs from multiple runs of ADMIXTURE |
| group_012_cnts | count up number of observed alleles in each group |
| hohz_windows_1 | compute fraction of heterozygous and homozygous and missing... |
| hwe_exact_test | perform exact tests of H-W disequilibrium for each locus... |
| mat_cumul_cpp | return a matrix of cumumlative sums along the rows or colums |
| miss_curves_indv | Order a genotype matrix by individual missingness at... |
| miss_curves_locus | Order a genotype matrix by locus missingness at different... |
| pairwise_fst | compute pairwise Fst using SNPRelate |
| pipe | Pipe operator |
| qprob_rando_raster | return an RGB raster of colors to depict breeding pops on a... |
| read_012 | read a set of 012 files from vcftools into a matrix of... |
| read_angsd_geno_probs | read an angsd binary genotype probability file |
| run_admixture | run admixture Reps times at each of K values |
| sample_from_angsd_probs | Sample a genotype (0,1,2) from probabilities for all the snps... |
| scan_012 | read a set of 012 files from vcftools into a matrix of... |
| slurp_admixture | read in all the AMIXTURE files that are in the r_X_K_Y... |
| testHWE | a quick function to do the HW exact test on on an open gds... |
