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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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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
unread,
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
unread,
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
unread,
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
Corin Stansfield
Mar 19
mqmscan Singular matrix error
Hi Karl, Danny and everyone else, I am also having a problem with the 'singular matrix' error
unread,
mqmscan Singular matrix error
Hi Karl, Danny and everyone else, I am also having a problem with the 'singular matrix' error
Mar 19
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
unread,
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
unread,
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
unread,
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,
unread,
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
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:
unread,
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
unread,
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
unread,
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
Ramesh Bhat
, …
Karl Broman
518
11/2/23
Single marker analysis with R/qtl
Okay, thank you. Sent from my iPhone On 02-Nov-2023, at 7:58 PM, Karl Broman <kbr...@gmail.com
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Single marker analysis with R/qtl
Okay, thank you. Sent from my iPhone On 02-Nov-2023, at 7:58 PM, Karl Broman <kbr...@gmail.com
11/2/23
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
Rachel Tavares
,
Karl Broman
4
10/17/23
Removing individual missing nearly all marker data
match() in this case is going to return a single value, and then is.na(match( ) ) is going to be
unread,
Removing individual missing nearly all marker data
match() in this case is going to return a single value, and then is.na(match( ) ) is going to be
10/17/23
Rachel Tavares
,
Karl Broman
3
10/16/23
Coverting physical location (bp) to Mbp
Thanks Karl! I did receive the warning and that's what made me realize the mistake. On Monday,
unread,
Coverting physical location (bp) to Mbp
Thanks Karl! I did receive the warning and that's what made me realize the mistake. On Monday,
10/16/23
Othmane Lamoumni
,
Karl Broman
3
10/8/23
Rqtl2 vs Rqtl
Thank you for your clarification I really appreciate the help Othmane On Sat, Oct 7, 2023, 21:15 Karl
unread,
Rqtl2 vs Rqtl
Thank you for your clarification I really appreciate the help Othmane On Sat, Oct 7, 2023, 21:15 Karl
10/8/23