summarize_stacks: summarize_stacks For each set of samples processed with...
| summarize_stacks | R Documentation |
summarize_stacks For each set of samples processed with populations (STACKS) and with vcf file generated for snps, this function creates a bash job file to calculate some basic popgen statistics.
Description
summarize_stacks
For each set of samples processed with populations (STACKS) and with vcf file generated for snps, this function creates a bash job file to calculate some basic popgen statistics.
Usage
summarize_stacks(dir, save = TRUE, use.popmap = FALSE, popmap = NULL)
Arguments
dir |
Directory containing multiple subdirectories, each of which contains the output files generated by populations (STACKS pipeline). |
save |
Logical indicating if the output should be saved. Default TRUE. |
use.popmap |
Logical indicating whether or not to assign individuals to different populations according to a population map. Default FALSE. |
popmap |
Character string to population map. Default NULL, in which case all individuals in 'save.in' are assigned to the same 'population'. |
Value
data frame with basic stats
