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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.txt | 2021-07-01 | 1.3 kB | |
| tests.poolSeq.R | 2021-07-01 | 6.5 kB | |
| Florida_123-Florida_23-N300-p050-simB.modified.sex.tab-simB-Florida_123-Mix1.snp-mimi-ds80x.sync | 2021-07-01 | 6.6 kB | |
| Florida_123-Florida_24-N300-p050-simB.modified.sex.tab-simB-Florida_123-Mix1.snp-mimi-ds80x.sync | 2021-07-01 | 6.6 kB | |
| Florida_123-Florida_175-N300-p050-simB.modified.sex.tab-simB-Florida_123-Mix1.snp-mimi-ds80x.sync | 2021-07-01 | 6.6 kB | |
| Florida_123-Florida_198-N300-p050-simB.modified.sex.tab-simB-Florida_123-Mix1.snp-mimi-ds80x.sync | 2021-07-01 | 6.6 kB | |
| 12082020-calcCMH.R | 2021-07-01 | 4.9 kB | |
| 30052020-1to1-calcAFandCOV.R | 2021-07-01 | 1.2 kB | |
| 30052020-1to1-wholeSYNC.R | 2021-07-01 | 4.5 kB | |
| Florida_123-Florida_14-N300-p050-simB.modified.sex.tab-simB-Florida_123-Mix1.snp-mimi-ds80x.sync | 2021-07-01 | 6.7 kB | |
| Totals: 10 Items | 51.5 kB | 0 | |
#Anna Maria Langmüller #Vetmeduni Vienna #05/2021 #Secondary E&R Sim #README: process-simulations processing of sync-files was done with the R-package poolSeq (v0.3.2) https://github.com/popgenvienna/poolSeq starting allele frequencies of targets were determined with the R-package poolSeq (v0.3.2) 30052020-1to1-wholeSYNC.R Example R-code to merge polymorphic data of single replicates of the 1to1 crossing scheme into 1 sync file output is stored as .rds object Uses *sync files *sync Dummy data (99 SNPs) for single replicates of the 1to1 crossing scheme of 1 simulation run 30052020-1to1-calcAFandCOV.R Example R-code to calculate allele frequencies for each SNP at each time-point and store as .rds object Note: although generated, sampled read depth and allele frequencies were not assessed in our analysis Uses .rds object generated with 30052020-1to1-wholeSYNC.R 12082020-calcCMH.R Example R-code to calculate CMH Test statistic and # of ties. Uses test.poolSeq.R and .rds object generated with 30052002-1to1-calcAFandCOV.R Please note that this code calculates CMH test statistics for a random SNP and not for a selected SNP tests.poolSeq.R Slightly modified code from the poolSeq R-Package to provide actual test statistics. This option is implemented in later versions of the R-package (e.g., v0.3.5).