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1–30 of 274
This group is for discussion about the use of
R/qtl2
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jcb...@gmail.com
,
Karl Broman
2
Jun 3
Allelic series number estimation
Consider the package TIMBR https://github.com/wesleycrouse/TIMBR See Crouse et al (2020) https://doi.
unread,
Allelic series number estimation
Consider the package TIMBR https://github.com/wesleycrouse/TIMBR See Crouse et al (2020) https://doi.
Jun 3
Karl Broman
Jun 2
R/qtl2 version 0.38
A new version of R/qtl2 (version 0.38) has been released on CRAN. Windows and Mac binaries will be
unread,
R/qtl2 version 0.38
A new version of R/qtl2 (version 0.38) has been released on CRAN. Windows and Mac binaries will be
Jun 2
Saikat Bandyopadhyay
,
Karl Broman
2
May 14
Porting analysis from mm10 to GRCm39
The mmconvert package has a function cross2_to_grcm39() to do exactly this, in cases where the
unread,
Porting analysis from mm10 to GRCm39
The mmconvert package has a function cross2_to_grcm39() to do exactly this, in cases where the
May 14
Saikat Bandyopadhyay
Apr 29
Correct way to group the mice samples based on the haplotype of a single location
I am analyzing bulk RNA seq data generated from the DO. I have genotype information for these and I
unread,
Correct way to group the mice samples based on the haplotype of a single location
I am analyzing bulk RNA seq data generated from the DO. I have genotype information for these and I
Apr 29
Fernando Andrade
,
Karl Broman
5
Apr 14
estimating gen maps
thanks! Em segunda-feira, 14 de abril de 2025 às 13:33:13 UTC-6, Karl Broman escreveu: Yes, the
unread,
estimating gen maps
thanks! Em segunda-feira, 14 de abril de 2025 às 13:33:13 UTC-6, Karl Broman escreveu: Yes, the
Apr 14
Fernando Andrade
, …
Dan Gatti
5
Mar 27
modifying DO allele probabilities
So, the rounding operation needs values multiplied by 2 to round correctly. Then you could divide the
unread,
modifying DO allele probabilities
So, the rounding operation needs values multiplied by 2 to round correctly. Then you could divide the
Mar 27
Michelle Lee
,
Dan Gatti
2
Mar 27
Generate sequence fasta for each DO mouse
I don't think that qtl2 provides this in a manner that's exposed to the user. For association
unread,
Generate sequence fasta for each DO mouse
I don't think that qtl2 provides this in a manner that's exposed to the user. For association
Mar 27
Bruno Saconi
,
Karl Broman
2
Mar 13
Phenotype data set up
For the analysis of recombinant inbred lines, I prefer to focus on strain means, as for QTL mapping
unread,
Phenotype data set up
For the analysis of recombinant inbred lines, I prefer to focus on strain means, as for QTL mapping
Mar 13
Luis Arge
,
Karl Broman
2
12/13/24
plotGeno with cross2 data
There's not any facility for converting data from cross2 to cross1 format. And unfortunately
unread,
plotGeno with cross2 data
There's not any facility for converting data from cross2 to cross1 format. And unfortunately
12/13/24
Saikat Bandyopadhyay
,
Karl Broman
5
10/3/24
Data for the plot_pxg()
Hi Dr Karl, I figured it out. I was looking to create a data frame where one of the columns is the
unread,
Data for the plot_pxg()
Hi Dr Karl, I figured it out. I was looking to create a data frame where one of the columns is the
10/3/24
Madi Shoken
,
Karl Broman
3
10/1/24
I got a position that does not exist
In the find_peaks function, if the maximum LOD score is hit at multiple positions, the position
unread,
I got a position that does not exist
In the find_peaks function, if the maximum LOD score is hit at multiple positions, the position
10/1/24
Jacky S
,
Karl Broman
2
9/9/24
issue with maxmarg() with QTLViewer data
I can't tell what's going wrong without having access to the data. karl On Monday, September
unread,
issue with maxmarg() with QTLViewer data
I can't tell what's going wrong without having access to the data. karl On Monday, September
9/9/24
Dor Fried
,
Karl Broman
4
8/28/24
Conversion from HAPPY (R1) to R/qtl2
Regarding the alternate allele, I would put a missing value. Regarding the mating history, I'm
unread,
Conversion from HAPPY (R1) to R/qtl2
Regarding the alternate allele, I would put a missing value. Regarding the mating history, I'm
8/28/24
manigben kulai amadu
,
Karl Broman
2
8/19/24
Plotting Chromosomal distribution of QTLs using qtl2 R package
The function plot_lodpeaks() is close. https://search.r-project.org/CRAN/refmans/qtl2/html/
unread,
Plotting Chromosomal distribution of QTLs using qtl2 R package
The function plot_lodpeaks() is close. https://search.r-project.org/CRAN/refmans/qtl2/html/
8/19/24
Saikat Bandyopadhyay
, …
Dan Gatti
4
8/6/24
Calculation of founder allele frequency at the chromosome level
I think that you can use the genoprobs from calc_genoprob() for this. You'd sum the frequencies
unread,
Calculation of founder allele frequency at the chromosome level
I think that you can use the genoprobs from calc_genoprob() for this. You'd sum the frequencies
8/6/24
Xinghua Li
,
Karl Broman
2
7/16/24
AIL genetic map construction
Genetic map estimation has not been implemented for AILs in R/qtl2. I agree that you could treat it
unread,
AIL genetic map construction
Genetic map estimation has not been implemented for AILs in R/qtl2. I agree that you could treat it
7/16/24
Fernando Andrade
,
Karl Broman
7
7/3/24
question on kinship correction and model comparison
Thank you! Em quarta-feira, 3 de julho de 2024 às 12:38:38 UTC-3, Karl Broman escreveu: If you leave
unread,
question on kinship correction and model comparison
Thank you! Em quarta-feira, 3 de julho de 2024 às 12:38:38 UTC-3, Karl Broman escreveu: If you leave
7/3/24
Chevreau Julien
,
Karl Broman
5
7/2/24
Chromosomes on physical and genetic maps
Right, ok. As I aligned the reads and used this information to infer the linkage groups, marker order
unread,
Chromosomes on physical and genetic maps
Right, ok. As I aligned the reads and used this information to infer the linkage groups, marker order
7/2/24
Saikat Bandyopadhyay
,
Karl Broman
3
7/1/24
Best way to extract scan data for a specific genomic range
Oops in the line calling scan1(), it should have iron$pheno in place of pheno out <- scan1(probs,
unread,
Best way to extract scan data for a specific genomic range
Oops in the line calling scan1(), it should have iron$pheno in place of pheno out <- scan1(probs,
7/1/24
Othmane Lamoumni
6/6/24
QTL co-detection
Hello everyone, When analyzing the same trait in multiple environments, detecting a consistent and
unread,
QTL co-detection
Hello everyone, When analyzing the same trait in multiple environments, detecting a consistent and
6/6/24
Sam Mantel
,
Karl Broman
3
6/5/24
High LOD scores across across the entire linkage map
I think the genotypes are confounded with cross, and so I would include cross covariate indicators in
unread,
High LOD scores across across the entire linkage map
I think the genotypes are confounded with cross, and so I would include cross covariate indicators in
6/5/24
Karl Broman
, …
Dan Gatti
15
5/29/24
R/qtl2 version 0.22
No. karl On Wednesday, May 29, 2024 at 6:11:56 AM UTC-5 Ramesh Bhat wrote: Yes, you are right. Is
unread,
R/qtl2 version 0.22
No. karl On Wednesday, May 29, 2024 at 6:11:56 AM UTC-5 Ramesh Bhat wrote: Yes, you are right. Is
5/29/24
lehong...@gmail.com
, …
Dan Gatti
11
5/24/24
Interaction in SNP association scan
Karl answered your question about scan1_blup(). eQTL mapping is largely the same as mapping a few
unread,
Interaction in SNP association scan
Karl answered your question about scan1_blup(). eQTL mapping is largely the same as mapping a few
5/24/24
Madi Shoken
,
Karl Broman
9
5/17/24
invalid genotypes in cross
You can ignore the warning. The heterozygote genotypes will be treated as missing. To avoid the
unread,
invalid genotypes in cross
You can ignore the warning. The heterozygote genotypes will be treated as missing. To avoid the
5/17/24
Jennifer Jacob
, …
Karl Broman
9
5/13/24
Error in convert_sex...
I have an FVB in there, so that is where the issue probably lies. As a non-DO, what is the best way
unread,
Error in convert_sex...
I have an FVB in there, so that is where the issue probably lies. As a non-DO, what is the best way
5/13/24
Karl Broman
5/13/24
R/qtl2 version 0.36
A new version of R/qtl2 (version 0.36) has been released on CRAN. Windows and Mac binaries will be
unread,
R/qtl2 version 0.36
A new version of R/qtl2 (version 0.36) has been released on CRAN. Windows and Mac binaries will be
5/13/24
Madi Shoken
,
Karl Broman
2
5/13/24
Markers with distorted segregation
calc_geno_freq() and calc_raw_geno_freq(). karl On Mon, May 13, 2024 at 2:55 AM Madi Shoken <
unread,
Markers with distorted segregation
calc_geno_freq() and calc_raw_geno_freq(). karl On Mon, May 13, 2024 at 2:55 AM Madi Shoken <
5/13/24
Madi Shoken
,
Karl Broman
4
5/4/24
Genetic map construction
Cross type is wheat RILs at F7 and the data is its genetic map. Thanks for the link, just found and
unread,
Genetic map construction
Cross type is wheat RILs at F7 and the data is its genetic map. Thanks for the link, just found and
5/4/24
Dan Gatti
4/16/24
RE: [EXTERNAL][WARNING: ATTACHMENT UNSCANNED][Rqtl2-disc] "write_control_file"
If you look closely at the error message, you'll see that you have a double path in there. I can
unread,
RE: [EXTERNAL][WARNING: ATTACHMENT UNSCANNED][Rqtl2-disc] "write_control_file"
If you look closely at the error message, you'll see that you have a double path in there. I can
4/16/24
Benjamin Van Raalte
,
Karl Broman
3
4/8/24
R/qtlDesign new implementation with R/qtl2
Karl, Thanks so much for the quick reply. I'll go ahead and use "R/qtlDesign" then. -
unread,
R/qtlDesign new implementation with R/qtl2
Karl, Thanks so much for the quick reply. I'll go ahead and use "R/qtlDesign" then. -
4/8/24