Calculate non-central statistic (NCD1)
ncd1.RdCalculate non-central statistic (NCD1)
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).
- tf
Target frequency.
- w
Window size in bp. Default is 3000.
- 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. Future implementation: "IS" defined windows around each informative site.
Value
A data.table object with columns: Win.ID, S (sites), IS (informative sites), tf (target frequency), ncd1
Examples
ncd1(x=ncd1_input, tf=0.5, w=3000, ncores=2, minIS=2)
#> Win.ID S IS tf ncd1
#> <char> <int> <int> <num> <num>
#> 1: 1_92_3092 20 20 0.5 0.4286047
#> 2: 1_1592_4592 21 21 0.5 0.4392331
#> 3: 1_3092_6092 15 15 0.5 0.4046166
#> 4: 1_4592_7592 12 12 0.5 0.3897881
#> 5: 1_6092_9092 19 19 0.5 0.3793086
#> 6: 1_7592_10592 28 28 0.5 0.3641235
#> 7: 1_9092_12092 25 25 0.5 0.3797493
#> 8: 1_10592_13592 15 15 0.5 0.4063328
#> 9: 1_12092_15092 25 25 0.5 0.3935370
#> 10: 1_13592_16592 30 30 0.5 0.3914497
#> 11: 1_15092_18092 22 22 0.5 0.4010361
#> 12: 1_16592_19592 18 18 0.5 0.4038215
#> 13: 1_18092_21092 11 11 0.5 0.4385437
#> 14: 1_19592_22592 15 15 0.5 0.4623715
#> 15: 1_21092_24092 20 20 0.5 0.4395955
#> 16: 1_22592_25592 16 16 0.5 0.4394827
#> 17: 1_24092_27092 17 17 0.5 0.4659706
#> 18: 1_25592_28592 20 20 0.5 0.4454260
#> 19: 1_27092_30092 22 22 0.5 0.4174539
#> 20: 1_28592_31592 12 12 0.5 0.4136724
#> Win.ID S IS tf ncd1