Man pages for surh/HMVAR
Human Microbiome Variant Analysis in R

benchmark_imputationBenchmark mice imputation
bimbam_imputeImpute genotypes with BIMBAM
calculate_prevalenceCalculate taxon prevalence
check_pvals_in_fileCheck p-values in MKtest.py outfile
check_pvaluesCheck p-values
determine_snp_distSNP distribution between sites
determine_snp_effectDetermine the effect of a coding variant on the aminoacid...
format_inputFormats input form HMMCP 16S files
format_input_hmqcpRead HMQCP input
gemma_kinshipCalculate kinship matrix with GEMMA
gemma_lmmRun LMM via GEMMA
genome_wide_niCalculate genome-wide NI and alpha
get_mk_results_filesGet files for MK results
get_site_distDetermine whether a variant site is fixed or polymorphic
mice_imputeImputation via mice
midas_mktestPerform McDonald-Kreitman test on MIDAS SNPs
midas_to_bimbamConvert MIDAS merge output to BIMBAM input
mkvaluesEntries in McDonald-Kreitman table.
phylotype2rdpFormat HMMCP phylotype taxonomy for AMOR
phylotype2rdp2Phylotype to RDP version 2
pval_qqplotp-value qqplot
read_midas_abunRead MIDAS abundance file
read_midas_dataRead midas snp merge data
run_commandRun system command
select_samples_from_abunSelect samples that are present in mapping file
tidy_miceTidy mice
surh/HMVAR documentation built on March 23, 2019, 12:11 a.m.