joe....@gmail.com
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to R/qtl discussion
I'm having trouble with read.cross() for type "4way", reading from a 'csvr' file. I get the error
1: In summary.cross(cross) :
The genetic maps should all be matrices with two rows.
Currently, I have my data formatted so that;
Col1 = markername
Col2 = chromosome id
Col3 = male map position
Col4 = female map position
(sample below)
But clearly this is not what read.cross() expects. I am unable to find any examples of a 'correctly formatted' 4way cross anywhere, and write.cross() will not allow the export of 4way crosses to csv format, so I can't see the correct way to format this so that read.cross() can read it as a matrix with two rows.
Any help would be appreciated.
test <- read.cross('csvr','.', 'test.txt', genotypes=NULL, estimate.map=FALSE, crosstype="4way")
head test.txt
id,,,,a,b,c,d,e,f
sex,,,,0,1,1,1,1,1,0,1,0,0,1,1,0,0,0
phe,,,,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
CHR2_288112,2,0.000,0.000,1,4,3,2,1,4
CHR2_334258,2,1.093,0.000,2,4,3,2,1,4
CHR2_334268,2,1.300,0.000,2,4,3,2,1,4
CHR2_455684,2,3.195,0.000,2,4,3,2,1,4
CHR2_517129,2,3.195,0.000,2,4,3,2,1,4
CHR2_740302,2,4.663,0.000,2,4,3,2,1,4