dos: Calculate Direction of Selection from SNV data
In surh/HMVAR: Human Microbiome Variant Analysis in R

Takes SNV data in MIDAS format and produces Direction of Selection (DoS) statistics.

dos(
  info,
  freq,
  depth,
  map,
  depth_thres = 1,
  freq_thres = 0.5,
  test = TRUE,
  clean = TRUE
)

`info`	Data table corresponding to the 'snps_info.txt' file from MIDAS. Must have columns 'site_id' and 'sample'
`freq`	A data table corresponding to the 'snps_freq.txt' file from MIDAS. Must have a 'site_id' column, and one more column per sample. Each row is the frequency of the minor allele for the corresponding site in the corresponding sample.
`depth`	A data table corresponding to the 'snps_depth.txt' file from MIDAS. Must have a 'site_id' column, and one more column per sample. Each row is the sequencing depth for the corresponding site in the corresponding sample.
`map`	A data table associating samples with groups (sites). must have columns 'sample' and 'Group'.
`depth_thres`	Minimum number of reads (depth) at a site at a sample to be considered.
`freq_thres`	Frequency cuttoff for minor vs major allele. The value represents the distance from 0 or 1, for a site to be assigned to the major or minor allele respectively. It must be a value in [0,1].
`test`	It TRUE, a Z-test will be performed on the DoS statistic.
`clean`	If TRUE, genes where DoS is undefined (either Dn and Ds are both zero, or Pn and Ps are both zero), will be removed from the result.

A tibble with the same columns as Dat plus a column named DoS. If test is passed, a column named p.value will also be included unless such a column already exists. In that case a column with the name DoS.p.value will be included

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.