Calculate non-central statistic (NCD2)
ncd2.RdCalculate non-central statistic (NCD2)
Arguments
- x
A data.table object with columns: CHR, POS, REF, ALT, tx_1 (number of alternate allele copies), tn_1 (total number of alleles), tx_2, and tn_2.
- tf
Target frequency. Any value between 0 and 0.5. Default is 0.5.
- w
Window size in bp. Default is 1000.
- ncores
Number of cores. Increasing this can speed things up for you. Default is 2.
- minIS
Minimum number of informative sites. Default is 2. Windows with less informative sites than this threshold are discarded.
- by
Define how to scan the genome. "POS" (default) defined sliding windows based on w. "IS" defined windows around each informative site.
Value
A data.table object with columns: Win.ID, S (sites), FD (fixed differences),IS (informative sites), tf (target frequency), ncd2
Examples
ncd2(x=ncd2_input, tf=0.5, w=3000, ncores=2, minIS=2)
#> Win.ID ncd2 S FD IS tf
#> <char> <num> <int> <int> <int> <num>
#> 1: 1_92_3092 0.4721648 20 29 49 0.5
#> 2: 1_1592_4592 0.4749101 21 28 49 0.5
#> 3: 1_3092_6092 0.4637019 15 22 37 0.5
#> 4: 1_4592_7592 0.4671135 12 25 37 0.5
#> 5: 1_6092_9092 0.4595906 19 33 52 0.5
#> 6: 1_7592_10592 0.4361486 28 27 55 0.5
#> 7: 1_9092_12092 0.4462502 25 27 52 0.5
#> 8: 1_10592_13592 0.4743746 15 36 51 0.5
#> 9: 1_12092_15092 0.4631460 25 42 67 0.5
#> 10: 1_13592_16592 0.4507518 30 32 62 0.5
#> 11: 1_15092_18092 0.4553608 22 24 46 0.5
#> 12: 1_16592_19592 0.4612429 18 24 42 0.5
#> 13: 1_18092_21092 0.4797632 11 21 32 0.5
#> 14: 1_19592_22592 0.4832595 15 18 33 0.5
#> 15: 1_21092_24092 0.4746826 20 26 46 0.5
#> 16: 1_22592_25592 0.4825311 16 37 53 0.5
#> 17: 1_24092_27092 0.4889201 17 34 51 0.5
#> 18: 1_25592_28592 0.4812203 20 36 56 0.5
#> 19: 1_27092_30092 0.4709149 22 37 59 0.5
#> 20: 1_28592_31592 0.4662210 12 17 29 0.5
#> Win.ID ncd2 S FD IS tf