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R/qtl discussion
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This group is for discussion about the use of
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Atoosa Samani
,
Karl Broman
5
Mar 3
error using addint function for mqm
I was able to reproduce the problem with the `fake.f2` dataset. It seems that `addint()` is not
unread,
error using addint function for mqm
I was able to reproduce the problem with the `fake.f2` dataset. It seems that `addint()` is not
Mar 3
Ellen R
,
Karl Broman
2
Feb 27
Plot without x-axis ticks/labels
Unfortunately, there's limited control over that sort of thing. So you're best bet is to make
unread,
Plot without x-axis ticks/labels
Unfortunately, there's limited control over that sort of thing. So you're best bet is to make
Feb 27
Lena Flörl
,
Karl Broman
8
Feb 16
Filter for significant phenotypes
Hi Karl - thanks a lot! On Wednesday, 15 February 2023 at 19:01:40 UTC-8 Karl Broman wrote: Those are
unread,
Filter for significant phenotypes
Hi Karl - thanks a lot! On Wednesday, 15 February 2023 at 19:01:40 UTC-8 Karl Broman wrote: Those are
Feb 16
Jason Johns
,
Karl Broman
2
Feb 12
plotlodprofile without using refineqtl
I think you'll have to just do this “by hand”. Loop over positions on the chromosome, call
unread,
plotlodprofile without using refineqtl
I think you'll have to just do this “by hand”. Loop over positions on the chromosome, call
Feb 12
Princia NAKOMBO
,
Karl Broman
2
Feb 6
QTL analysis_distorsion segregation
I would not omit the heterozygotes, particularly as they are 25% of the data. I don't understand
unread,
QTL analysis_distorsion segregation
I would not omit the heterozygotes, particularly as they are 25% of the data. I don't understand
Feb 6
Rohan Richard
, …
Martin Ferris
5
Feb 3
Scantwo function output interpretation
I've found, to decrease the computational time, I can decrease my marker density to save on
unread,
Scantwo function output interpretation
I've found, to decrease the computational time, I can decrease my marker density to save on
Feb 3
Thomas Blankers
,
Karl Broman
3
Feb 1
fitqtl effect estimates for X chromosome
Thanks! Op donderdag 26 januari 2023 om 15:45:55 UTC+1 schreef kbr...@gmail.com: Unfortunately,
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fitqtl effect estimates for X chromosome
Thanks! Op donderdag 26 januari 2023 om 15:45:55 UTC+1 schreef kbr...@gmail.com: Unfortunately,
Feb 1
Lena Flörl
,
Karl Broman
5
Jan 31
Multiple phenotypes: multivariate regression vs loop over single traits
Dear Karl, thanks a lot for the explanation - I'll have a closer look at the p-values then!
unread,
Multiple phenotypes: multivariate regression vs loop over single traits
Dear Karl, thanks a lot for the explanation - I'll have a closer look at the p-values then!
Jan 31
Martin Ferris
,
Karl Broman
2
Jan 27
conversion functions
No there isn't; sorry. karl On Friday, January 27, 2023 at 9:08:56 AM UTC-6 martin....@gmail.com
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conversion functions
No there isn't; sorry. karl On Friday, January 27, 2023 at 9:08:56 AM UTC-6 martin....@gmail.com
Jan 27
Princia NAKOMBO
,
Karl Broman
3
Jan 20
Two scan qtl
Hello, i have 175 individuals and 941 markers princia Le lundi 16 janvier 2023 à 16:36:01 UTC+1, kbr.
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Two scan qtl
Hello, i have 175 individuals and 941 markers princia Le lundi 16 janvier 2023 à 16:36:01 UTC+1, kbr.
Jan 20
Arasi
,
Karl Broman
2
Jan 18
determine the source that contributes the allele for particular QTL?
You can use the functions plotPXG() or effectplot() to plot the phenotype vs the genotype at a locus.
unread,
determine the source that contributes the allele for particular QTL?
You can use the functions plotPXG() or effectplot() to plot the phenotype vs the genotype at a locus.
Jan 18
Karl Broman
Jan 7
R/qtl version 1.58
A new version of R/qtl (1.58) has been released at its website (https://rqtl.org) and on CRAN.
unread,
R/qtl version 1.58
A new version of R/qtl (1.58) has been released at its website (https://rqtl.org) and on CRAN.
Jan 7
Karl Broman
12/1/22
R/qtl version 1.54
A new version of R/qtl (1.54) has been released at its website (https://rqtl.org) and on CRAN.
unread,
R/qtl version 1.54
A new version of R/qtl (1.54) has been released at its website (https://rqtl.org) and on CRAN.
12/1/22
Tiago Ribeiro
,
Karl Broman
2
11/29/22
Additive dominance model
R/qtl doesn't have any facility for additive or dominance models. And for RIL, it omits and
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Additive dominance model
R/qtl doesn't have any facility for additive or dominance models. And for RIL, it omits and
11/29/22
Etienne Dvorak
,
Karl Broman
4
11/29/22
Markers at the wrong end of a linkage group
orderMarkers() uses a pretty simplistic method. I don't think it's worth thinking too hard
unread,
Markers at the wrong end of a linkage group
orderMarkers() uses a pretty simplistic method. I don't think it's worth thinking too hard
11/29/22
Ellen Risemberg
,
Karl Broman
3
11/8/22
perm.strata vs addcovar in scanoneperm
This makes sense, thanks! On Tuesday, November 1, 2022 at 10:16:39 AM UTC-4 kbr...@gmail.com wrote:
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perm.strata vs addcovar in scanoneperm
This makes sense, thanks! On Tuesday, November 1, 2022 at 10:16:39 AM UTC-4 kbr...@gmail.com wrote:
11/8/22
Princia NAKOMBO
,
Karl Broman
9
11/3/22
Use of countXO or locateX0
You can start with physical distances, but it's maybe best to provide Mbp rather than bp
unread,
Use of countXO or locateX0
You can start with physical distances, but it's maybe best to provide Mbp rather than bp
11/3/22
xu4...@gmail.com
,
Karl Broman
3
11/2/22
function plot.pxg not found in version 1.52
Got it! Thanks! On Wednesday, November 2, 2022 at 1:16:00 PM UTC-5 kbr...@gmail.com wrote: It was
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function plot.pxg not found in version 1.52
Got it! Thanks! On Wednesday, November 2, 2022 at 1:16:00 PM UTC-5 kbr...@gmail.com wrote: It was
11/2/22
Tiago Ribeiro
,
Karl Broman
3
10/28/22
Simulating genotype skew
It is an intercross (F12), I suspect that one of the two parental inbred strains might have produced
unread,
Simulating genotype skew
It is an intercross (F12), I suspect that one of the two parental inbred strains might have produced
10/28/22
Ramesh Bhat
, …
Karl Broman
510
10/15/22
Single marker analysis with R/qtl
No, there isn't. karl On Saturday, October 15, 2022 at 3:48:04 AM UTC-5 Ramesh Bhat wrote: Is
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Single marker analysis with R/qtl
No, there isn't. karl On Saturday, October 15, 2022 at 3:48:04 AM UTC-5 Ramesh Bhat wrote: Is
10/15/22
shepher...@gmail.com
,
Karl Broman
2
10/14/22
Remove redundant markers
There's a function findDupMarkers() for identifying markers with identical data. There's also
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Remove redundant markers
There's a function findDupMarkers() for identifying markers with identical data. There's also
10/14/22
Tiago Ribeiro
,
Karl Broman
2
10/3/22
LOD score permutation too high?
Significance thresholds for two-dimensional scan can be large. They depend principally on genome size
unread,
LOD score permutation too high?
Significance thresholds for two-dimensional scan can be large. They depend principally on genome size
10/3/22
Tiago Ribeiro
,
Karl Broman
2
9/25/22
scantwo permutation - parallelization
You need to make sure that each run gets a different seed. What I do is use set.seed() with a large
unread,
scantwo permutation - parallelization
You need to make sure that each run gets a different seed. What I do is use set.seed() with a large
9/25/22
laavanya rayaprolu
,
Karl Broman
4
9/6/22
Missing phenotypes
They can be used as “NA”. You should get identical results. karl On Tuesday, September 6, 2022 at 3:
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Missing phenotypes
They can be used as “NA”. You should get identical results. karl On Tuesday, September 6, 2022 at 3:
9/6/22
David O'Donnell
,
Lipps, Sarah J
2
8/4/22
Random sampling in R to obtain a p-value
Hi David, I am uncertain how to do this using r/qtl, but this can be done on the command line using
unread,
Random sampling in R to obtain a p-value
Hi David, I am uncertain how to do this using r/qtl, but this can be done on the command line using
8/4/22
Tiago Ribeiro
,
Martin Ferris
2
8/2/22
cM distance
Karl will have to confirm, but c should influence the a* and k* estimates between pairs of markers. I
unread,
cM distance
Karl will have to confirm, but c should influence the a* and k* estimates between pairs of markers. I
8/2/22
David
, …
Lara
13
7/21/22
mqmscan singular matrix
Thanks, I updated the package and re-ran checkAlleles() with markerlrt(). It returned that there are
unread,
mqmscan singular matrix
Thanks, I updated the package and re-ran checkAlleles() with markerlrt(). It returned that there are
7/21/22
Karl Broman
7/9/22
R/qtl version 1.52
A new version of R/qtl (1.52) has been released at its website (https://rqtl.org) and on CRAN.
unread,
R/qtl version 1.52
A new version of R/qtl (1.52) has been released at its website (https://rqtl.org) and on CRAN.
7/9/22
mukesh choudhary
,
Karl Broman
4
7/1/22
Coding of the markers for SNP markers where parents have heterozygous condition?
R/qtl is developed for crosses between inbred lines, and can't handle heterozygosity in the
unread,
Coding of the markers for SNP markers where parents have heterozygous condition?
R/qtl is developed for crosses between inbred lines, and can't handle heterozygosity in the
7/1/22
Jen
, …
mukesh choudhary
9
6/30/22
dominant markers and formLinkageGroups()
Can you please help me with how the coding was fixed for dominant markers? I am struggling with my
unread,
dominant markers and formLinkageGroups()
Can you please help me with how the coding was fixed for dominant markers? I am struggling with my
6/30/22