Hi Lang,
I think qtl is a contributed R package, but not a Bioconductor
package. So you should probably be following the advice on the
'posting guide'
http://www.r-project.org/posting-guide.html
and try to contact the package author first (use library(help=qtl) to
find the author contact info). If that fails, try sending email to
R-help.
Looking at the documentation for read.cross
>?read.cross
there's a section on the csv format. The last paragraph says
The cross is determined to be a backcross if only the first two
elements of the 'genotypes' string are found; otherwise, it is
assumed to be an intercross.
this is a little cryptic, but I think what it is saying is that in a
design like
AA x BB --> AB
Backcross, e.g., to AA --> only AA, AB
So if at each locus only two genotypes AA and AB are observed, then
the experiment is classified as a 'backcross'. I guess in your data at
least some loci have more than two genotypes. Perhaps this is an input
data format error.
Looking at the checkrf procedure indicated in the warning
> checkrf
it seems like the code is looking that the information for each marker
is somehow 'reasonable'. Finding that it isn't, it suggests one
possible reason. Again, this looks like a data input format error.
Hope that helps,
Martin
"Lang Chen" <lchen at="" ms.soph.uab.edu=""> writes:
> 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]]
>
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