Skip to content

Commit

Permalink
ped kinship added
Browse files Browse the repository at this point in the history
  • Loading branch information
@SamGurr
SamGurr committed Jan 30, 2025
1 parent 3836d78 commit ba4ee34
Show file tree
Hide file tree
Showing 6 changed files with 678 additions and 264 deletions.
215 changes: 215 additions & 0 deletions RAnalysis/Output/Popgen/pedigree/All_Low_v_Moderate_final.csv
View file

Large diffs are not rendered by default.

252 changes: 128 additions & 124 deletions RAnalysis/Output/Popgen/pedigree/F0BF1O/F0BF1O_kinship.csv
View file

Large diffs are not rendered by default.

248 changes: 124 additions & 124 deletions RAnalysis/Output/Popgen/pedigree/F0BF1O/F0BF1O_ped.csv
View file
Original file line number Diff line number Diff line change
@@ -1,124 +1,124 @@
"id","fid","mid","sex"
"adapter_trim.F0-B1.bam","0","0",0
"adapter_trim.F0-B10.bam","0","0",1
"adapter_trim.F0-B11.bam","0","0",0
"adapter_trim.F0-B13.bam","0","0",1
"adapter_trim.55.bam","adapter_trim.F0-B13.bam","adapter_trim.F0-B11.bam",0
"adapter_trim.F0-B14.bam","0","0",1
"adapter_trim.254.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B11.bam",0
"adapter_trim.F0-B15.bam","0","0",2
"adapter_trim.351.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B15.bam",0
"adapter_trim.F0-B16.bam","0","0",1
"adapter_trim.F0-B17.bam","0","0",2
"adapter_trim.5.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B17.bam",0
"adapter_trim.303.bam","adapter_trim.F0-B1.bam","adapter_trim.F0-B17.bam",0
"adapter_trim.253.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B17.bam",0
"adapter_trim.153.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B17.bam",0
"adapter_trim.F0-B18.bam","0","0",2
"adapter_trim.F0-B2.bam","0","0",0
"adapter_trim.F0-B20.bam","0","0",1
"adapter_trim.F0-B21.bam","0","0",2
"adapter_trim.352.bam","adapter_trim.F0-B11.bam","adapter_trim.F0-B21.bam",0
"adapter_trim.F0-B22.bam","0","0",2
"adapter_trim.201.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B22.bam",0
"adapter_trim.F0-B25.bam","0","0",2
"adapter_trim.F0-B26.bam","0","0",1
"adapter_trim.304.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B2.bam",0
"adapter_trim.251.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B22.bam",0
"adapter_trim.101.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F0-B27.bam","0","0",1
"adapter_trim.F0-B3.bam","0","0",0
"adapter_trim.204.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.103.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B3.bam",0
"adapter_trim.F0-B4.bam","0","0",0
"adapter_trim.54.bam","adapter_trim.F0-B4.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.301.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B4.bam",0
"adapter_trim.F0-B5.bam","0","0",2
"adapter_trim.F0-B6.bam","0","0",2
"adapter_trim.353.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B6.bam",0
"adapter_trim.3.bam","adapter_trim.F0-B27.bam","adapter_trim.F0-B6.bam",0
"adapter_trim.F0-B7.bam","0","0",0
"adapter_trim.53.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B7.bam",0
"adapter_trim.4.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B7.bam",0
"adapter_trim.203.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B7.bam",0
"adapter_trim.104.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B21.bam",0
"adapter_trim.F0-B9.bam","0","0",2
"adapter_trim.155.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B9.bam",0
"adapter_trim.154.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B9.bam",0
"adapter_trim.F1-B1-pH75.bam","adapter_trim.F0-B27.bam","adapter_trim.F0-B9.bam",2
"adapter_trim.F1-B1-pH8.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B25.bam",2
"adapter_trim.F1-B10-pH8.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B7.bam",2
"adapter_trim.F1-B11-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B5.bam",1
"adapter_trim.F1-B11-pH8.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B2.bam",2
"adapter_trim.F1-B12-pH75.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B3.bam",1
"adapter_trim.F1-B14-pH75.bam","adapter_trim.F0-B11.bam","adapter_trim.F0-B22.bam",2
"adapter_trim.F1-B15-pH8.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B6.bam",1
"adapter_trim.F1-B16-pH75.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B5.bam",1
"adapter_trim.F1-B17-pH75.bam","adapter_trim.F0-B13.bam","adapter_trim.F0-B1.bam",1
"adapter_trim.F1-B20-pH75.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B6.bam",2
"adapter_trim.F1-B20-pH8.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B3.bam",1
"adapter_trim.F1-B21-pH75.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B25.bam",1
"adapter_trim.F1-B21-pH8.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B2.bam",1
"adapter_trim.F1-B25-pH8.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B22.bam",1
"adapter_trim.F1-B3-pH8.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B1.bam",2
"adapter_trim.F1-B4-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B2.bam",2
"adapter_trim.F1-B4-pH8.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B6.bam",2
"adapter_trim.F1-B5-pH8.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B9.bam",2
"adapter_trim.F1-B6-pH75.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B25.bam",1
"adapter_trim.F1-B7-pH8.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B2.bam",2
"adapter_trim.F1-B8-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B21.bam",2
"adapter_trim.F1-B8-pH8.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-B9-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B22.bam",2
"adapter_trim.F1-B9-pH8.bam","adapter_trim.F0-B4.bam","adapter_trim.F0-B25.bam",2
"adapter_trim.F1-J105-pH8.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B3.bam",0
"adapter_trim.F1-J106-pH8.bam","adapter_trim.F0-B4.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-J110-pH8.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B15.bam",0
"adapter_trim.F1-J111-pH8.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J112-pH8.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B11.bam",0
"adapter_trim.F1-J113-pH8.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B9.bam",0
"adapter_trim.F1-J114-pH8.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B2.bam",0
"adapter_trim.F1-J13-pH8.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B6.bam",0
"adapter_trim.F1-J14-pH8.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B11.bam",0
"adapter_trim.F1-J157-pH8.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B1.bam",0
"adapter_trim.F1-J158-pH8.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B15.bam",0
"adapter_trim.F1-J16-pH8.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B9.bam",0
"adapter_trim.F1-J160-pH8.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J161-pH8.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B17.bam",0
"adapter_trim.F1-J162-pH8.bam","adapter_trim.F0-B13.bam","adapter_trim.F0-B4.bam",0
"adapter_trim.F1-J163-pH8.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J164-pH8.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B11.bam",0
"adapter_trim.F1-J17-pH8.bam","adapter_trim.F0-B11.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J18-pH8.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B15.bam",0
"adapter_trim.F1-J205-pH75.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J206-pH75.bam","adapter_trim.F0-B11.bam","adapter_trim.F0-B15.bam",0
"adapter_trim.F1-J207-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B4.bam",0
"adapter_trim.F1-J209-pH75.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B5.bam",0
"adapter_trim.F1-J210-pH75.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B3.bam",0
"adapter_trim.F1-J212-pH75.bam","adapter_trim.F0-B13.bam","adapter_trim.F0-B22.bam",0
"adapter_trim.F1-J255-pH75.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B1.bam",0
"adapter_trim.F1-J258-pH75.bam","adapter_trim.F0-B11.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J259-pH75.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B4.bam",0
"adapter_trim.F1-J261-pH75.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B1.bam",0
"adapter_trim.F1-J262-pH75.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B5.bam",0
"adapter_trim.F1-J263-pH75.bam","adapter_trim.F0-B13.bam","adapter_trim.F0-B5.bam",0
"adapter_trim.F1-J264-pH75.bam","adapter_trim.F0-B27.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-J306-pH75.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J307-pH75.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J308-pH75.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B1.bam",0
"adapter_trim.F1-J311-pH75.bam","adapter_trim.F0-B11.bam","adapter_trim.F0-B9.bam",0
"adapter_trim.F1-J312-pH75.bam","adapter_trim.F0-B26.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-J313-pH75.bam","adapter_trim.F0-B4.bam","adapter_trim.F0-B5.bam",0
"adapter_trim.F1-J314-pH75.bam","adapter_trim.F0-B10.bam","adapter_trim.F0-B7.bam",0
"adapter_trim.F1-J356-pH75.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B21.bam",0
"adapter_trim.F1-J361-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B5.bam",0
"adapter_trim.F1-J362-pH75.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B1.bam",0
"adapter_trim.F1-J363-pH75.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-J364-pH75.bam","adapter_trim.F0-B13.bam","adapter_trim.F0-B11.bam",0
"adapter_trim.F1-J372-pH75.bam","adapter_trim.F0-B14.bam","adapter_trim.F0-B1.bam",0
"adapter_trim.F1-J6-pH8.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B4.bam",0
"adapter_trim.F1-J65-pH8.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-J66-pH8.bam","adapter_trim.F0-B16.bam","adapter_trim.F0-B7.bam",0
"adapter_trim.F1-J67-pH8.bam","adapter_trim.F0-B2.bam","adapter_trim.F0-B25.bam",0
"adapter_trim.F1-J68-pH8.bam","adapter_trim.F0-B7.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J69-pH8.bam","adapter_trim.F0-B3.bam","adapter_trim.F0-B18.bam",0
"adapter_trim.F1-J70-pH8.bam","adapter_trim.F0-B20.bam","adapter_trim.F0-B9.bam",0
"V1","V2","V3","V4"
1,0,0,0
2,0,0,1
3,0,0,0
4,0,0,1
5,4,3,0
6,0,0,1
7,6,3,0
8,0,0,2
9,2,8,0
10,0,0,1
11,0,0,2
12,2,11,0
13,1,11,0
14,2,11,0
15,6,11,0
16,0,0,2
17,0,0,0
18,0,0,1
19,0,0,2
20,3,19,0
21,0,0,2
22,2,21,0
23,0,0,2
24,0,0,1
25,24,17,0
26,24,21,0
27,24,16,0
28,0,0,1
29,0,0,0
30,29,16,0
31,18,29,0
32,0,0,0
33,32,23,0
34,10,32,0
35,0,0,2
36,0,0,2
37,6,36,0
38,28,36,0
39,0,0,0
40,2,39,0
41,2,39,0
42,2,39,0
43,39,19,0
44,0,0,2
45,10,44,0
46,18,44,0
47,28,44,2
48,2,23,2
49,18,39,2
50,18,35,1
51,6,17,2
52,24,29,1
53,3,21,2
54,29,36,1
55,29,35,1
56,4,1,1
57,2,36,2
58,18,29,1
59,2,23,1
60,6,17,1
61,18,21,1
62,10,1,2
63,18,17,2
64,17,36,2
65,24,44,2
66,2,23,1
67,10,17,2
68,18,19,2
69,17,23,0
70,18,21,2
71,32,23,2
72,2,29,0
73,32,23,0
74,24,8,0
75,39,16,0
76,24,3,0
77,17,44,0
78,6,17,0
79,29,36,0
80,18,3,0
81,6,1,0
82,39,8,0
83,17,44,0
84,29,16,0
85,6,11,0
86,4,32,0
87,10,16,0
88,10,3,0
89,3,16,0
90,6,8,0
91,39,16,0
92,3,8,0
93,18,32,0
94,17,35,0
95,6,29,0
96,4,21,0
97,2,1,0
98,3,16,0
99,6,32,0
100,24,1,0
101,39,35,0
102,4,35,0
103,28,23,0
104,39,16,0
105,6,16,0
106,10,1,0
107,3,44,0
108,24,23,0
109,32,35,0
110,2,39,0
111,39,19,0
112,18,35,0
113,18,1,0
114,29,23,0
115,4,3,0
116,6,1,0
117,10,32,0
118,17,23,0
119,10,39,0
120,17,23,0
121,39,16,0
122,29,16,0
123,18,44,0
77 changes: 76 additions & 1 deletion RAnalysis/Scripts/Popgen/06_pedigree.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,7 @@ Remember that our experiment ran fir three generations! Here is a best foot forw
F0BF1O.vcf <- All.vcf[,c(1:26,63:139, 27:62)] # 138 samples, 2,947 variants, 16 chromosomes
# F1 broodstock and F2 offspring (treatment specific!)
F1BF2O_LOW.vcf <- All.vcf[,c(1, 27:45, 198:218, 152:163)] # ??? samples, 2,947 variants, 16 chromosomes
F1BF2O_LOW.vcf <- All.vcf[,c(1, 27:45, 198:218, 153:163)] # ??? samples, 2,947 variants, 16 chromosomes
F1BF2O_MOD.vcf <- All.vcf[,c(1, 46:62, 219:250, 164:177)] # ??? samples, 2,947 variants, 16 chromosomes
F1BF2O_HIGH.vcf <- All.vcf[,c(1, 27:45, 178:197, 140:152)] # ??? samples, 2,947 variants, 16 chromosomes
Expand All @@ -232,6 +232,12 @@ F2BF3O_LOW.vcf <- All.vcf[,c(1, 152:163, 295:343)] # ??? samples, 2,947 variant
F2BF3O_MOD.vcf <- All.vcf[,c(1, 164:177, 344:392)] # ??? samples, 2,947 variants, 16 chromosomes
F2BF3O_HIGH.vcf <- All.vcf[,c(1, 140:152, 251:294)] # ??? samples, 2,947 variants, 16 chromosomes
# F0 thorugh F3 low and moderate only!
All_LOW_MOD.vcf <- All.vcf[,c(1:139, # F0 and all F1 offspring
153:163, 198:218, # F2 offspring from low OA
164:177, 219:250, # F2 offspring from moderate OA
295:343, # F3 offspring from low OA
344:392)] # F3 offspring from moderate OA
```


Expand Down Expand Up @@ -265,6 +271,11 @@ F2BF3O_MOD.gen <- F2BF3O_MOD.vcf %>% vcfR2genind()
# HIGH F2 parents and their F3 offspring
F2BF3O_HIGH.gen <- F2BF3O_HIGH.vcf %>% vcfR2genind()
# F0 thorugh F3 low and moderate only! :::::::::::::::::::::::::::::::
All_LOW_MOD.gen <- All_LOW_MOD.vcf %>% vcfR2genind()
```

# **Sequoia**
Expand Down Expand Up @@ -349,6 +360,9 @@ F2BF3O_LOW.ListIDs <- colnames(F2BF3O_LOW.vcf@gt[,2:length(colnames(F2BF3O_LO
F2BF3O_MOD.ListIDs <- colnames(F2BF3O_MOD.vcf@gt[,2:length(colnames(F2BF3O_MOD.vcf@gt))])
F2BF3O_HIGH.ListIDs <- colnames(F2BF3O_HIGH.vcf@gt[,2:length(colnames(F2BF3O_HIGH.vcf@gt))])
# F0 through F3 low and moderate only! :::::::::::::::::::::::::::::::
All_LOW_MOD.ListIDs <- colnames(All_LOW_MOD.vcf@gt[,2:length(colnames(All_LOW_MOD.vcf@gt))])
```

* GenoM
Expand All @@ -369,6 +383,9 @@ F1BF2O_HIGH.GenoM <- as.matrix(F1BF2O_HIGH.gen)
F2BF3O_LOW.GenoM <- as.matrix(F2BF3O_LOW.gen)
F2BF3O_MOD.GenoM <- as.matrix(F2BF3O_MOD.gen)
F2BF3O_HIGH.GenoM <- as.matrix(F2BF3O_HIGH.gen)
# F0 through F3 low and moderate only! :::::::::::::::::::::::::::::::
All_LOW_MOD.GenoM <- as.matrix(All_LOW_MOD.gen)
```

* LifeHistData
Expand Down Expand Up @@ -503,6 +520,12 @@ F2BF3O <- dplyr::filter(All.LifeHistData, grepl(c("F2-B|F3"),
F2BF3O_LOW.LifeHistData <- dplyr::filter(F2BF3O, grepl("pH8", ID))
F2BF3O_MOD.LifeHistData <- dplyr::filter(F2BF3O, grepl("pH75", ID))
F2BF3O_HIGH.LifeHistData <- dplyr::filter(F2BF3O, grepl("pH7\\.", ID))
# F0 through F3 low and moderate only! :::::::::::::::::::::::::::::::
All_LOW_MOD.LifeHistData <- dplyr::filter(All.LifeHistData, !grepl("pH7\\.", ID)) # all but pH7 data
```

* Pedigree
Expand Down Expand Up @@ -686,6 +709,13 @@ return(list(raw = pedigree.raw,
# FIRST SANITY CHECK THAT GENOM HAS ALL IDS OF LIFEHISTDATA
# F0 thorugh F3 LOW and MODERATE only!!
sort(rownames(All_LOW_MOD.GenoM)) == sort(All_LOW_MOD.LifeHistData$ID) # falses here
All_LOW_MOD.GenoM_final <- All_LOW_MOD.GenoM[row.names(All_LOW_MOD.GenoM) %in% All_LOW_MOD.LifeHistData$ID, ] # force it
sort(rownames(All_LOW_MOD.GenoM_final)) == sort(All_LOW_MOD.LifeHistData$ID) # now true
# F0 AND F1 OFFPSRING ALL ::::::::::::::::::::::::::::::::::::::::::
sort(rownames(F0BF1O.GenoM)) == sort(F0BF1O.LifeHistData$ID) # falses here
F0BF1O.GenoM_final <- F0BF1O.GenoM[row.names(F0BF1O.GenoM) %in% F0BF1O.LifeHistData$ID, ] # force it
Expand Down Expand Up @@ -732,6 +762,51 @@ sort(rownames(F1BF2O_MOD.GenoM_final)) == sort(F1BF2O_MOD.LifeHistData$ID)
```

* run BootPed for all low and moderate animals F0 through F3

inputs:
- GenoM = All_LOW_MOD.GenoM_final
- LifeHistData = All_LOW_MOD.LifeHistData
- threshold.LLR = -2
- min.LLR = 0.1
- n.SNP = 50
- n.bootstrap = 20

output:


```{r BootPed run all low and moderate individuals}
# F0 AND F1 OFFPSRING ALL ::::::::::::::::::::::::::::::::::::::::::
All_Low_Mod.sequoia <- BootPed(
All_LOW_MOD.GenoM_final, # GenoM
All_LOW_MOD.LifeHistData, # LifeHistData
-2,# threshold.LLR
0.1,# min.LLR
50, # n.SNP
150 # n.bootstrap
)
# data files
All_Low_Mod.pedigree.raw <- as.data.frame(All_Low_Mod.sequoia$raw)
rownames(All_Low_Mod.pedigree.raw) <- NULL # renomve rownames
All_Low_Mod.pedigree.summary <- as.data.frame(All_Low_Mod.sequoia$summary)
rownames(All_Low_Mod.pedigree.summary) <- NULL # renomve rownames
All_Low_Mod.pedigree.summary <- apply(All_Low_Mod.pedigree.summary,2,as.character) # need to do this to output the list of batches!
All_Low_Mod.pedigree.final <- as.data.frame(All_Low_Mod.pedigree.summary) %>%
group_by(id) %>% # group by id - there are mutliple occurances of pedigree assign for ids!
filter(Fertilization_pairs %in% 'TRUE') %>%
dplyr::top_n(1, absLLRtotal) %>% # take the best hit essential, highest LLR total
dplyr::select(id, dam, sire, absLLRtotal, dam.batch, sire.batch, Fertilization_pairs, loci) # select the target columns for next sequoia run
rownames(All_Low_Mod.pedigree.final) <- NULL # renomve rownames
write.csv(All_Low_Mod.pedigree.final, "RAnalysis/Output/Popgen/pedigree/All_Low_v_Moderate_final.csv")
```


* run BootPed for F0BF1J

inputs:
Expand Down
Loading

0 comments on commit ba4ee34

Please sign in to comment.