midas_dos: Direction of Selection statistics on MIDAS output
In surh/HMVAR: Human Microbiome Variant Analysis in R

Take output from MIDAS script midas_merge.py and obtain and test Direction of Selection (DoS) statistics.

midas_dos(
  midas_dir,
  map,
  map_file,
  genes = NULL,
  depth_thres = 1,
  freq_thres = 0.5,
  focal_group = NA
)

`midas_dir`	Directory where the output from midas_merge.py is located. It must include files: 'snps_info.txt', 'snps_depth.txt' and 'snps_freq.txt'.
`map`	Either a file path or a tibble. If a path, it mos point to a mapping file associating samples in the MIDAS otput to groups. It must have an 'ID' and a 'Group' column. If a tibble. It must have columns 'sample' and 'Group'.
`map_file`	Same as map. Present for backwards compatibility.
`genes`	The list of genes that are to be tested. Must correspond to entries in the 'genes_id' column of the 'snps_info.txt' file. If NULL, all genes will be tested.
`depth_thres`	The minimum number of reads at a position in a given sample for that position in that sample to be included.
`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].
`focal_group`	A string indicating the group that should be compared to everything else. If different from NA, all values in the 'Group' column of the mapping file will be converted to "non.<focal_group>", ensuring a dichotomous grouping.