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R/qtl discussion
1–30 of 1304
This group is for discussion about the use of
R/qtl
. The related
announcements group
provides only announcements of software updates. For discussion about
R/qtl2
, see the
rqtl2-disc group
.
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Ramesh Bhat
, …
Karl Broman
559
May 6
Single marker analysis with R/qtl
If you know chromosome and positions of markers, yes include them in the input file. I wouldn't
unread,
Single marker analysis with R/qtl
If you know chromosome and positions of markers, yes include them in the input file. I wouldn't
May 6
Birgül Güden
,
Karl Broman
6
May 5
The problem of linkage map larger than 1000 cm
R/qtl has a function est.map() for re-estimating inter-marker distances. karl On Monday, May 5, 2025
unread,
The problem of linkage map larger than 1000 cm
R/qtl has a function est.map() for re-estimating inter-marker distances. karl On Monday, May 5, 2025
May 5
vega....@gmail.com
,
Karl Broman
3
Mar 27
lodint using cim results
Thank you! is there a better more precise approach? I plan to use lodint with the output of cim as I
unread,
lodint using cim results
Thank you! is there a better more precise approach? I plan to use lodint with the output of cim as I
Mar 27
Adrianna Jurek
,
Karl Broman
6
Mar 21
Sex as an Interactive Covariate
What I meant, in doing it by hand, is something like the following: for(i in 1:1000) { tempx <-
unread,
Sex as an Interactive Covariate
What I meant, in doing it by hand, is something like the following: for(i in 1:1000) { tempx <-
Mar 21
Adrianna Jurek
,
Karl Broman
7
Mar 18
F2 cross and pgm
Great! Thank you so much for your quick and helpful responses, I very much appreciate it. Adrianna On
unread,
F2 cross and pgm
Great! Thank you so much for your quick and helpful responses, I very much appreciate it. Adrianna On
Mar 18
Adrianna Jurek
,
Karl Broman
3
Mar 17
X'X Matrix is Singular, X Chr issues
I do not seem to have the same issue running "hk" instead of "ehk". There are no
unread,
X'X Matrix is Singular, X Chr issues
I do not seem to have the same issue running "hk" instead of "ehk". There are no
Mar 17
N I
,
Karl Broman
2
Feb 24
Confused about data types
I think it is likely fine to treat it as a continuous measurement. R/qtl doesn't have any special
unread,
Confused about data types
I think it is likely fine to treat it as a continuous measurement. R/qtl doesn't have any special
Feb 24
Forest Hunt
Jan 16
Confused about scanone and scantwo with different results
I have an F1 population with ~250 grape individuals which I am testing for the presence of color
unread,
Confused about scanone and scantwo with different results
I have an F1 population with ~250 grape individuals which I am testing for the presence of color
Jan 16
Meiling Wong
,
Karl Broman
5
Jan 9
Interpreting p-values and LOD scores from fitqtl output.
Thank you so much Karl! On Wed, Jan 8, 2025 at 11:59 AM Karl Broman <kbr...@gmail.com> wrote:
unread,
Interpreting p-values and LOD scores from fitqtl output.
Thank you so much Karl! On Wed, Jan 8, 2025 at 11:59 AM Karl Broman <kbr...@gmail.com> wrote:
Jan 9
Luigi Faino
, …
Samuel Wang
8
12/27/24
make a genitic map from zero
Dear L: What methods were used to generate the genotype data? If the genotype data were generated
unread,
make a genitic map from zero
Dear L: What methods were used to generate the genotype data? If the genotype data were generated
12/27/24
Helene Grindeland
,
Karl Broman
2
11/19/24
Mapping of a qualitative trait
Generally, there's no inherent problem, in QTL mapping, with using very dense markers, as the
unread,
Mapping of a qualitative trait
Generally, there's no inherent problem, in QTL mapping, with using very dense markers, as the
11/19/24
Lena Flörl
,
Karl Broman
6
11/1/24
Bayes Credible Interval is zero or negative?
The interval should contain the peak LOD. I can't explain what is going on without seeing the
unread,
Bayes Credible Interval is zero or negative?
The interval should contain the peak LOD. I can't explain what is going on without seeing the
11/1/24
Siri B
,
Karl Broman
3
10/17/24
Long and gappy map
Dear Karl, Thank you so much for your quick reply. After further analysis of our data, we suspect
unread,
Long and gappy map
Dear Karl, Thank you so much for your quick reply. After further analysis of our data, we suspect
10/17/24
Nathaniel Burner
10/16/24
MQM fixed residual variance
Hi Karl, I am having trouble understanding how MQM fixes residual error to that of the full model as
unread,
MQM fixed residual variance
Hi Karl, I am having trouble understanding how MQM fixes residual error to that of the full model as
10/16/24
Lena Flörl
,
Karl Broman
3
10/2/24
QTLs at markers with high entropy / variance
In regions with low entropy and low variance, you have little genotype information and so low power
unread,
QTLs at markers with high entropy / variance
In regions with low entropy and low variance, you have little genotype information and so low power
10/2/24
Forest Hunt
,
Karl Broman
2
9/23/24
Would a MYB factor switch be considered a covariate?
You can include the genotype of that location as an additive covariate. There's an example of
unread,
Would a MYB factor switch be considered a covariate?
You can include the genotype of that location as an additive covariate. There's an example of
9/23/24
Karl Broman
8/21/24
R/qtl version 1.70
A new version of R/qtl (1.70) has been released at its website (https://rqtl.org) and on CRAN.
unread,
R/qtl version 1.70
A new version of R/qtl (1.70) has been released at its website (https://rqtl.org) and on CRAN.
8/21/24
Muhammad Habib Widyawan
,
Karl Broman
2
8/14/24
PVE more than 100%
The PVE estimates provided by fitqtl is just a transformation of the LOD score, and only account for
unread,
PVE more than 100%
The PVE estimates provided by fitqtl is just a transformation of the LOD score, and only account for
8/14/24
Lena Flörl
,
Karl Broman
3
7/26/24
Can changing the step size in conditional genotype probabilities lead to different results?
Hi Karl, thanks a lot for the super quick reply! Yes, I do permutation testing (1000 permutations)
unread,
Can changing the step size in conditional genotype probabilities lead to different results?
Hi Karl, thanks a lot for the super quick reply! Yes, I do permutation testing (1000 permutations)
7/26/24
HECTOR LOPEZ MORENO
6/18/24
stepwise error with 4way cross in small population
Hi Karl, I am writing to you about a problem I am having with stepwise and that has already been
unread,
stepwise error with 4way cross in small population
Hi Karl, I am writing to you about a problem I am having with stepwise and that has already been
6/18/24
Siri B
5/30/24
ASMAP error in lods subscript out of bounds
Hi, We have been stuck on a problem with pushcross() in asmap for a while. (I know asmap is
unread,
ASMAP error in lods subscript out of bounds
Hi, We have been stuck on a problem with pushcross() in asmap for a while. (I know asmap is
5/30/24
Robert Mattera
,
Karl Broman
4
5/19/24
Results of Scantwo (with permutations) of different phenotypes is the Same
You can use saveRDS() and readRDS() to save/read a single R object to/from an .rds file. You can use
unread,
Results of Scantwo (with permutations) of different phenotypes is the Same
You can use saveRDS() and readRDS() to save/read a single R object to/from an .rds file. You can use
5/19/24
PAWANDEEP Singh
,
Karl Broman
5
5/14/24
epistasis or additive effect
Thanks for the reply On Tue, May 14, 2024, 18:55 Karl Broman <kbr...@gmail.com> wrote: I use
unread,
epistasis or additive effect
Thanks for the reply On Tue, May 14, 2024, 18:55 Karl Broman <kbr...@gmail.com> wrote: I use
5/14/24
Corin Stansfield
,
Karl Broman
2
5/3/24
PVE formulas
The results from fitqtl are not more sophisticated than the formula you cite. In fact, we just use
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PVE formulas
The results from fitqtl are not more sophisticated than the formula you cite. In fact, we just use
5/3/24
Maunveri
,
Karl Broman
2
4/24/24
Renaming linkage groups (map construction)?
You can change the names of the chromosomes by assigning a vector of character strings to names(
unread,
Renaming linkage groups (map construction)?
You can change the names of the chromosomes by assigning a vector of character strings to names(
4/24/24
Joshua Havill
,
Karl Broman
2
4/18/24
Simulating Switched Alleles and Segregation Distortion
You can simulate most anything, provided you have a probability model. And you'll need to write
unread,
Simulating Switched Alleles and Segregation Distortion
You can simulate most anything, provided you have a probability model. And you'll need to write
4/18/24
Richard Merrill
,
Karl Broman
4
4/15/24
qtlDesign not available for newer versions of R
The qtlDesign package is again available at CRAN, https://cran.r-project.org/package=qtlDesign karl
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qtlDesign not available for newer versions of R
The qtlDesign package is again available at CRAN, https://cran.r-project.org/package=qtlDesign karl
4/15/24
Maunveri
, …
Karl Broman
5
4/8/24
QTL detected in single-QTL scan disappears cim
The genotype associations may also show up in a plot of pairwise recombination fractions using est.rf
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QTL detected in single-QTL scan disappears cim
The genotype associations may also show up in a plot of pairwise recombination fractions using est.rf
4/8/24
Othmane Lamoumni
3/23/24
Investigation of QTL intervals
Hello everyone, I apologize for addressing a topic out of R/qtl applications, but I would like to
unread,
Investigation of QTL intervals
Hello everyone, I apologize for addressing a topic out of R/qtl applications, but I would like to
3/23/24
Othmane Lamoumni
,
Karl Broman
3
3/21/24
Variance explained
Indeed, I've come to check the function description. It states these estimations can be
unread,
Variance explained
Indeed, I've come to check the function description. It states these estimations can be
3/21/24