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