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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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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
Ramesh Bhat
, …
Karl Broman
538
May 3
Single marker analysis with R/qtl
Thank you so much. Kind regards, On Fri, May 3, 2024 at 11:09 AM Karl Broman <kbr...@gmail.com
unread,
Single marker analysis with R/qtl
Thank you so much. Kind regards, On Fri, May 3, 2024 at 11:09 AM Karl Broman <kbr...@gmail.com
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
PAWANDEEP Singh
,
Karl Broman
2
Apr 22
epistasis or additive effect
Statistical geneticists generally use the term “epistasis” to mean any departure from additivity. So
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epistasis or additive effect
Statistical geneticists generally use the term “epistasis” to mean any departure from additivity. So
Apr 22
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
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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
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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
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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
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Rationale behind convert2riself genotype conversion
Just trying to guess at which are the correct genotype labels. Most commonly, the data initially get
Feb 9
venkat rami reddy
, …
Karl Broman
6
Feb 5
QTL Effects after running scanone()
I don't have enough information to be able to answer these questions. karl On Feb 5, 2024, at 6:
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QTL Effects after running scanone()
I don't have enough information to be able to answer these questions. karl On Feb 5, 2024, at 6:
Feb 5
Rachel Tavares
,
Karl Broman
4
Feb 2
Plotting all LOD scores and markers
I don't know what could be going wrong. If you try the following example, does it look correct?
unread,
Plotting all LOD scores and markers
I don't know what could be going wrong. If you try the following example, does it look correct?
Feb 2
Neda Rahnamae
, …
Karl Broman
5
Jan 30
Dominant or additive locus
Think of AA, AB, and BB genotypes having average phenotypes -a, +d, and +a, respectively. For a
unread,
Dominant or additive locus
Think of AA, AB, and BB genotypes having average phenotypes -a, +d, and +a, respectively. For a
Jan 30
Othmane Lamoumni
, …
Karl Broman
6
Jan 16
QTL Multi-model
Thank you Dr.Broman I've already thought of and looped the stepwiseqtl function to maximize the
unread,
QTL Multi-model
Thank you Dr.Broman I've already thought of and looped the stepwiseqtl function to maximize the
Jan 16
Lise H
,
Karl Broman
2
12/22/23
Missing genotypic information in 4-way cross
For the “4way” cross type in R/qtl, you need to infer phase in each individual, which means
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Missing genotypic information in 4-way cross
For the “4way” cross type in R/qtl, you need to infer phase in each individual, which means
12/22/23
Rachel Tavares
12/21/23
Gact/UTL package for calling SNPs
Hi Karl, I am working to use the Gact/UTL package to convert my vcf files (founders and samples) into
unread,
Gact/UTL package for calling SNPs
Hi Karl, I am working to use the Gact/UTL package to convert my vcf files (founders and samples) into
12/21/23
Othmane Lamoumni
12/15/23
To multiple QTL analysis
Hello everyone, I would just like your help for confirming some of my conclusions: 1- (IM) as a
unread,
To multiple QTL analysis
Hello everyone, I would just like your help for confirming some of my conclusions: 1- (IM) as a
12/15/23
Karl Broman
11/27/23
R/qtl version 1.66
A new version of R/qtl (1.66) has been released at its website (https://rqtl.org) and on CRAN.
unread,
R/qtl version 1.66
A new version of R/qtl (1.66) has been released at its website (https://rqtl.org) and on CRAN.
11/27/23
Karl Broman
11/17/23
R/qtl version 1.62
A new version of R/qtl (1.62) has been released at its website (https://rqtl.org) and on CRAN.
unread,
R/qtl version 1.62
A new version of R/qtl (1.62) has been released at its website (https://rqtl.org) and on CRAN.
11/17/23
Tomohiro.M
,
Karl Broman
2
11/10/23
How to create a graph that displays the LOD score threshold separately for autosome and sex chromosome
Use the function add.threshold() add.threshold(out.1, perms=operm.1, alpha=0.05, col="red")
unread,
How to create a graph that displays the LOD score threshold separately for autosome and sex chromosome
Use the function add.threshold() add.threshold(out.1, perms=operm.1, alpha=0.05, col="red")
11/10/23
林宥任
,
Karl Broman
2
11/9/23
One of my Linkage Group Started from 50cM
You can use the function shiftmap() to shift the starting position of all chromosomes to 0. karl On
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One of my Linkage Group Started from 50cM
You can use the function shiftmap() to shift the starting position of all chromosomes to 0. karl On
11/9/23
Rachel Tavares
,
Karl Broman
2
10/23/23
Removing alternative alleles not found in parent samples
I'm not sure I understand the context, as in R/qtl1, the genotypes have to be coded like A/H/B
unread,
Removing alternative alleles not found in parent samples
I'm not sure I understand the context, as in R/qtl1, the genotypes have to be coded like A/H/B
10/23/23