Commit e6f58f7a authored by mariefbourdon's avatar mariefbourdon
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220623 calc for reviewing

parent 6930f0b3
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......@@ -285,5 +285,8 @@ The two markers before the pseudomarker have an excess of homozygous.
```{r save_narrow}
save(pheno_before_annot_data2,peak7,peak7_tab,file="data2_peaks.rda")
tab2_data2 <- tab2
save(tab2_data2,file="tab2_data2.rda")
rm(tab2_data2)
```
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......@@ -121,8 +121,13 @@ write_rqtl(geno=genos,pheno=phenos,tab=tab2,ref=strains,par1="StrainA",par2="Str
cross_after <- read.cross(format="csv",file="cluster/cross_after.csv",
genotypes=c("0","1"),na.strings=c("NA"), convertXdata=TRUE)
## calc geno prob
cross_after <- calc.genoprob(cross_after, step=2.0, off.end=0.0,
error.prob=1.0E-4, map.function="haldane", stepwidth="fixed")
## calculate est map
newmap_after <- est.map(cross=cross_after,error.prob=0.01)
load("cluster/newmap_after.rda")
plotMap(cross_after,newmap_after,shift=TRUE)
tab2 <- mark_estmap(tab=tab2,map=newmap_after,annot=annot_mini)
......@@ -137,8 +142,12 @@ write_rqtl(geno=genos,pheno=phenos,tab=tab2,ref=strains,par1="StrainA",par2="Str
cross_after2 <- read.cross(format="csv",file="cluster2/cross_after2.csv",
genotypes=c("0","1"),na.strings=c("NA"), convertXdata=TRUE)
# load rda with newmap
load("cluster2/newmap_after2.rda")
## calc geno prob
cross_after2 <- calc.genoprob(cross_after2, step=2.0, off.end=0.0,
error.prob=1.0E-4, map.function="haldane", stepwidth="fixed")
## calculate est map
newmap_after2 <- est.map(cross=cross_after2,error.prob=0.01)
# plot
plotMap(cross_after2,newmap_after2,shift=TRUE)
......@@ -205,4 +214,7 @@ rm(none,allele,match,poly,prop)
```{r}
pheno_before_data3 <- pheno_before_plot
save(pheno_before_data3,file="data3_peaks.rda")
tab2_data3 <- tab2
save(tab2_data3,file="tab2_data3.rda")
rm(tab2_data3)
```
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......@@ -528,5 +528,8 @@ geno_plot12
```{r}
save(pheno_before_annot_data4,peak11,peak11_tab,file="data4_peaks.rda")
tab2_data4 <- tab2
save(tab2_data4,file="tab2_data4.rda")
rm(tab2_data4)
```
article/distrib_freq_rec1.png

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