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This group is for discussion about the use of
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Helene Grindeland
,
Karl Broman
2
Nov 19
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
Nov 19
Ramesh Bhat
, …
Karl Broman
557
Nov 13
Single marker analysis with R/qtl
One approach would be to change the chromosome IDs in the input data file. Alternatively, you change
unread,
Single marker analysis with R/qtl
One approach would be to change the chromosome IDs in the input data file. Alternatively, you change
Nov 13
Lena Flörl
,
Karl Broman
6
Nov 1
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
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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
Nov 1
Siri B
,
Karl Broman
3
Oct 17
Long and gappy map
Dear Karl, Thank you so much for your quick reply. After further analysis of our data, we suspect
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Long and gappy map
Dear Karl, Thank you so much for your quick reply. After further analysis of our data, we suspect
Oct 17
Nathaniel Burner
Oct 16
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
Oct 16
Lena Flörl
,
Karl Broman
3
Oct 2
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
Oct 2
Forest Hunt
,
Karl Broman
2
Sep 23
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
Sep 23
Karl Broman
Aug 21
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.
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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.
Aug 21
Muhammad Habib Widyawan
,
Karl Broman
2
Aug 14
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
Aug 14
Lena Flörl
,
Karl Broman
3
Jul 26
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)
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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)
Jul 26
HECTOR LOPEZ MORENO
Jun 18
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
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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
Jun 18
Siri B
May 30
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
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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
May 30
Robert Mattera
,
Karl Broman
4
May 19
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
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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
May 19
PAWANDEEP Singh
,
Karl Broman
5
May 14
epistasis or additive effect
Thanks for the reply On Tue, May 14, 2024, 18:55 Karl Broman <kbr...@gmail.com> wrote: I use
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epistasis or additive effect
Thanks for the reply On Tue, May 14, 2024, 18:55 Karl Broman <kbr...@gmail.com> wrote: I use
May 14
Corin Stansfield
,
Karl Broman
2
May 3
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
May 3
Maunveri
,
Karl Broman
2
Apr 24
Renaming linkage groups (map construction)?
You can change the names of the chromosomes by assigning a vector of character strings to names(
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Renaming linkage groups (map construction)?
You can change the names of the chromosomes by assigning a vector of character strings to names(
Apr 24
Joshua Havill
,
Karl Broman
2
Apr 18
Simulating Switched Alleles and Segregation Distortion
You can simulate most anything, provided you have a probability model. And you'll need to write
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Simulating Switched Alleles and Segregation Distortion
You can simulate most anything, provided you have a probability model. And you'll need to write
Apr 18
Richard Merrill
,
Karl Broman
4
Apr 15
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
Apr 15
Maunveri
, …
Karl Broman
5
Apr 8
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
Apr 8
Othmane Lamoumni
Mar 23
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
Mar 23
Othmane Lamoumni
,
Karl Broman
3
Mar 21
Variance explained
Indeed, I've come to check the function description. It states these estimations can be
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Variance explained
Indeed, I've come to check the function description. It states these estimations can be
Mar 21
edb...@gmail.com
Mar 20
Speed up genetic map - estimate.map function
Hi all, I have a file with 30k markers and is taking a long time to estimate.map function to run. How
unread,
Speed up genetic map - estimate.map function
Hi all, I have a file with 30k markers and is taking a long time to estimate.map function to run. How
Mar 20
Eric González
,
Karl Broman
2
Mar 18
read a genetic map into r/qtl
Yes, exactly; flip.order is precisely the function to use. I'd forgotten it existed. Here's
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read a genetic map into r/qtl
Yes, exactly; flip.order is precisely the function to use. I'd forgotten it existed. Here's
Mar 18
Tami Hildahl
, …
Karl Broman
5
Mar 15
Jittering and additional peaks
Ah, very good. Yes, that would work. thanks, karl On Fri, Mar 15, 2024 at 6:06 AM Othmane Lamoumni
unread,
Jittering and additional peaks
Ah, very good. Yes, that would work. thanks, karl On Fri, Mar 15, 2024 at 6:06 AM Othmane Lamoumni
Mar 15
Nathaniel Burner
,
Karl Broman
2
Mar 11
MQM scan window size
Personally I don't like the whole windowing business in CIM. I think those tall tight peaks with
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MQM scan window size
Personally I don't like the whole windowing business in CIM. I think those tall tight peaks with
Mar 11
Nathaniel Burner
2
Mar 8
Singular Matrix in MQM
Removing duplicate markers resolved this issue. This is an F5 population and I removed duplicate
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Singular Matrix in MQM
Removing duplicate markers resolved this issue. This is an F5 population and I removed duplicate
Mar 8
Nathaniel Burner
,
Karl Broman
2
Mar 7
CIM with multiple phenotypes
The cim() function can take only a single phenotype column at a time. You can specify it with either
unread,
CIM with multiple phenotypes
The cim() function can take only a single phenotype column at a time. You can specify it with either
Mar 7
Nathaniel Burner
,
Karl Broman
2
Feb 19
switch.order removes pulled markers from cross
pullCross appears to be an ASMap function. If it's putting extra information in the cross object,
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switch.order removes pulled markers from cross
pullCross appears to be an ASMap function. If it's putting extra information in the cross object,
Feb 19
Harisa Muratovic
,
Karl Broman
5
Feb 15
Genotype encoded as 0 and 1
Cross type affects the imputation of missing genotype information, at markers and in-between markers,
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Genotype encoded as 0 and 1
Cross type affects the imputation of missing genotype information, at markers and in-between markers,
Feb 15
Nathaniel Burner
,
Karl Broman
2
Feb 9
Rationale behind convert2riself genotype conversion
Just trying to guess at which are the correct genotype labels. Most commonly, the data initially get
unread,
Rationale behind convert2riself genotype conversion
Just trying to guess at which are the correct genotype labels. Most commonly, the data initially get
Feb 9