Hi,

 

I am learning the R/qtl. I have two questions. 1)The data is the inbreed
line of Drosophila. Why the R.qtl shows F2 intercross. 2) what did the
warnings tell me?

 

Thank you,

 

Lang

 

Here is the case:

 

> library(qtl)

> dat=read.cross("csv", file="rqtl_trt.csv")

 --Read the following data:

         75  individuals

         80  markers

         1  phenotypes

> summary(dat)

    F2 intercross

 

    No. individuals:  75 

 

    No. phenotypes:   1 

    Percent phenotyped:  100 

 

    No. chromosomes:  4 

    Total markers:    80 

    No. markers:      17 20 3 40 

    Percent genotyped:  100 

    Genotypes (%):      AA:41.3  AB:4.7  BB:54  not BB:0  not AA:0 

 

> dat <- est.rf(dat)

There were 45 warnings (use warnings() to see them)

> warnings()

Warning messages:

1: Genotypes potentially switched for marker 3E (2) on chr 1

 in: checkrf(cross, 3) 

2: Genotypes potentially switched for marker 4F (3) on chr 1

 in: checkrf(cross, 3) 

3: Genotypes potentially switched for marker 5D (4) on chr 1

 in: checkrf(cross, 3) 

4: Genotypes potentially switched for marker 6E (5) on chr 1

 in: checkrf(cross, 3) 

5: Genotypes potentially switched for marker 11C (10) on chr 1

 in: checkrf(cross, 3) 

6: Genotypes potentially switched for marker 11D (11) on chr 1

 in: checkrf(cross, 3) 

7: Genotypes potentially switched for marker 12E (12) on chr 1

 in: checkrf(cross, 3) 

8: Genotypes potentially switched for marker 14C (13) on chr 1

 in: checkrf(cross, 3) 

9: Genotypes potentially switched for marker 15A (14) on chr 1

 in: checkrf(cross, 3) 

10: Genotypes potentially switched for marker 16D (15) on chr 1

 in: checkrf(cross, 3) 

11: Genotypes potentially switched for marker 17C (16) on chr 1

 in: checkrf(cross, 3) 

12: Genotypes potentially switched for marker 19A (17) on chr 1

 in: checkrf(cross, 3) 

13: Genotypes potentially switched for marker 34EF (8) on chr 2

 in: checkrf(cross, 3) 

14: Genotypes potentially switched for marker 35B (9) on chr 2

 in: checkrf(cross, 3) 

15: Genotypes potentially switched for marker 38A (10) on chr 2

 in: checkrf(cross, 3) 

16: Genotypes potentially switched for marker 38E (11) on chr 2

 in: checkrf(cross, 3) 

17: Genotypes potentially switched for marker 43A (12) on chr 2

 in: checkrf(cross, 3) 

18: Genotypes potentially switched for marker 43E (13) on chr 2

 in: checkrf(cross, 3) 

19: Genotypes potentially switched for marker 46A (14) on chr 2

 in: checkrf(cross, 3) 

20: Genotypes potentially switched for marker 46C (15) on chr 2

 in: checkrf(cross, 3) 

21: Genotypes potentially switched for marker 48D (16) on chr 2

 in: checkrf(cross, 3) 

22: Genotypes potentially switched for marker 49D (17) on chr 2

 in: checkrf(cross, 3) 

23: Genotypes potentially switched for marker 50B (18) on chr 2

 in: checkrf(cross, 3) 

24: Genotypes potentially switched for marker 50D (19) on chr 2

 in: checkrf(cross, 3) 

25: Genotypes potentially switched for marker 50F (20) on chr 2

 in: checkrf(cross, 3) 

26: Genotypes potentially switched for marker 57F (2) on chr 3

 in: checkrf(cross, 3) 

27: Genotypes potentially switched for marker 60E (3) on chr 3

 in: checkrf(cross, 3) 

28: Genotypes potentially switched for marker 77E (16) on chr 4

 in: checkrf(cross, 3) 

29: Genotypes potentially switched for marker 82D (18) on chr 4

 in: checkrf(cross, 3) 

30: Genotypes potentially switched for marker 87B (21) on chr 4

 in: checkrf(cross, 3) 

31: Genotypes potentially switched for marker 87E (22) on chr 4

 in: checkrf(cross, 3) 

32: Genotypes potentially switched for marker 87F (23) on chr 4

 in: checkrf(cross, 3) 

33: Genotypes potentially switched for marker 88E (24) on chr 4

 in: checkrf(cross, 3) 

34: Genotypes potentially switched for marker 89B (25) on chr 4

 in: checkrf(cross, 3) 

35: Genotypes potentially switched for marker 91A (26) on chr 4

 in: checkrf(cross, 3) 

36: Genotypes potentially switched for marker 91D (27) on chr 4

 in: checkrf(cross, 3) 

37: Genotypes potentially switched for marker 93A (29) on chr 4

 in: checkrf(cross, 3) 

38: Genotypes potentially switched for marker 93B (30) on chr 4

 in: checkrf(cross, 3) 

39: Genotypes potentially switched for marker 94D (31) on chr 4

 in: checkrf(cross, 3) 

40: Genotypes potentially switched for marker 96A (32) on chr 4

 in: checkrf(cross, 3) 

41: Genotypes potentially switched for marker 96F (33) on chr 4

 in: checkrf(cross, 3) 

42: Genotypes potentially switched for marker 97D (34) on chr 4

 in: checkrf(cross, 3) 

43: Genotypes potentially switched for marker 97E (35) on chr 4

 in: checkrf(cross, 3) 

44: Genotypes potentially switched for marker 98A (36) on chr 4

 in: checkrf(cross, 3) 

45: Genotypes potentially switched for marker 99A (37) on chr 4

 in: checkrf(cross, 3) 

> 


	[[alternative HTML version deleted]]

