Commit 99dc483f authored by Marie Bourdon's avatar Marie Bourdon
Browse files

article figures

parent adc44da6
Warning messages:
1: In fixXgeno.f2(cross, alleles) :
--Omitting 236 male heterozygote genotypes on the X chromosome.
2: In fixXgeno.f2(cross, alleles) :
--There appear to be some individuals of each cross direction, but "pgm" is not provided.
Check the X chr genotype data and include a "pgm" column in the phenotype data.
"pgm" was inferred (probably poorly).
3: In summary.cross(cross) :
Some markers at the same position on chr 1,2,5,6,7,8,9,10,11,12,13,14,15,17,18,19,X; use jittermap().
Warning message:
In est.map(cross = cross_after, error.prob = 0.01) : Didn't converge!
Warning message:
In matchchr(chr, names(x$geno)) : Chr Y not found
--Read the following data:
176 individuals
2236 markers
4 phenotypes
--Cross type: f2
#!/bin/sh
#SBATCH -J "after"
#SBATCH --qos=normal
#SBATCH --mem=1000
#SBATCH -o after.out -e after.err
#SBATCH --mail-type=END --mail-user=mbourdon@pasteur.fr
Rscript after.R || exit 1
exit 0
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% latex table generated in R 4.1.0 by xtable 1.8-4 package
% Tue Aug 3 11:29:00 2021
\begin{table}[ht]
\centering
\begin{tabular}{lllllrrr}
\hline
marker & parent1 & parent2 & allele\_1 & allele\_2 & n\_HM1 & n\_HM2 & n\_HT \\
\hline
S6J010381992 & T & T & T & C & 52.00 & 24.00 & 83.00 \\
S6J011498219 & T & T & T & G & 52.00 & 33.00 & 86.00 \\
S6H012742425 & G & G & A & G & 30.00 & 52.00 & 94.00 \\
mUNC010317552 & G & G & A & G & 34.00 & 67.00 & 75.00 \\
gUNC1973125 & T & T & T & C & 67.00 & 34.00 & 74.00 \\
S6J032196596 & A & A & A & G & 45.00 & 41.00 & 74.00 \\
\hline
\end{tabular}
\end{table}
......@@ -175,9 +175,6 @@ The cross object was saved in stuart. Here we can load it as well as the newmap
```{r load_cross}
library(qtl)
# stuart_cross <- read.cross(format="csv",file="../stuart_cross.csv",
# genotypes=c("0","1","2"),na.strings=c("NA"), convertXdata=TRUE)
# save(stuart_cross,file="../stuart_cross.rda")
data(stuart_cross)
summary(stuart_cross)
......
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