Julie Kim
unread,Jan 3, 2019, 1:15:05 PM1/3/19Sign in to reply to author
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to R/qtl discussion
Dr. Karl,
After loading in the genotype data set into R with read.cross(), I am trying to figure out what is the best way to map the markers for an F2 intercross. I followed the manual for genetic map construction with R/qtl, and tried these functions:
> lg <- formLinkageGroups(mapthis, max.rf=0.35, min.lod=6)
> table(lg[,2])
but when I plot
> plotRF(mapthis, alternate.chrid=TRUE)
to see how well it worked, the plot is not anywhere close to the example plot in the manual.
Here is my code (I tried ordering markers on chromosome 5):
> lg <- formLinkageGroups(map_athaf, max.rf=0.35, min.lod=13)
Warning message:
In formLinkageGroups(map_athaf, max.rf = 0.35, min.lod = 13) :
Running est.rf.
> table(lg[,2])
1 2 3 4 5
207 106 97 85 4
> map_athaf_lg <- formLinkageGroups(map_athaf, max.rf=0.35, min.lod=13, reorgMarkers=TRUE)
Warning message:
In formLinkageGroups(map_athaf, max.rf = 0.35, min.lod = 13, reorgMarkers = TRUE) :
Running est.rf.
> plotRF(map_athaf_lg, alternate.chrid=TRUE)
> map_athaf_chr5 <- orderMarkers(map_athaf_lg, chr=5)
> pull.map(map_athaf_chr5, chr=5)
30.1_CHR_5_544767 30.1_CHR_5_1283613 30.1_CHR_5_1283633 30.1_CHR_5_1297106
0.0000000 0.4163351 0.4163486 0.4163621
I then came across another discussion on the google group, and I wondered whether I should be doing this:
#####################
#### listeria data, pretending we don't know chr assignments or marker order
# load listeria data
data(listeria)
# omit the X chromosome
listeria <- subset(listeria, chr="-X")
# markers not on chr 1
mnames <- markernames(listeria, chr="-1")
# move them to chr 1
for(i in mnames)
listeria <- movemarker(listeria, i, 1)
# randomize marker order
listeria <- switch.order(listeria, chr=1, order=sample(totmar(listeria)))
#### estimate pairwise recombination fractions
listeria <- est.rf(listeria)
plot.rf(listeria)
#### establish linkage groups
revlisteria <- formLinkageGroups(listeria, reorgMarkers=TRUE)
plot.rf(revlisteria)
#### determine marker order on each chromosome
revlisteria <- orderMarkers(revlisteria, verbose=TRUE)
plot.rf(revlisteria)
#####################
What would be the best way to go about ordering the markers? Thank you so much for your help!