Man pages for eriqande/genoscapeRtools
Tools for building migratory bird genoscapes

compile_assayablereturn SNPs and say whether the are assayable or not, along...
comp_pairmake a comparison between two groups that are in df
convert_012_to_bedcreate a PLINK bed file from and 012 matrix
correct_ass_probfrom vectors of snp allele freqs, compute the expected prob...
geno_freq_calcsfrom on 012 file compute expected and observed genotype...
geno_freq_calc_singlefrom on 012 file compute expected and observed genotype...
genoscape_pcado a PCA using SNPRelate and prepare output for rapid...
genoscapeRtoolsMy package documentation <e2><80><a6> bla bla <e2><80><a6>
ggplot_the_Qsggplot the Qs from multiple runs of ADMIXTURE
group_012_cntscount up number of observed alleles in each group
hohz_windows_1compute fraction of heterozygous and homozygous and missing...
hwe_exact_testperform exact tests of H-W disequilibrium for each locus...
mat_cumul_cppreturn a matrix of cumumlative sums along the rows or colums
miss_curves_indvOrder a genotype matrix by individual missingness at...
miss_curves_locusOrder a genotype matrix by locus missingness at different...
pairwise_fstcompute pairwise Fst using SNPRelate
pipePipe operator
qprob_rando_rasterreturn an RGB raster of colors to depict breeding pops on a...
read_012read a set of 012 files from vcftools into a matrix of...
read_angsd_geno_probsread an angsd binary genotype probability file
run_admixturerun admixture Reps times at each of K values
sample_from_angsd_probsSample a genotype (0,1,2) from probabilities for all the snps...
scan_012read a set of 012 files from vcftools into a matrix of...
slurp_admixtureread in all the AMIXTURE files that are in the r_X_K_Y...
testHWEa quick function to do the HW exact test on on an open gds...
eriqande/genoscapeRtools documentation built on Feb. 5, 2018, 4:37 p.m.