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R/qtl2 discussion

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This group is for discussion about the use of R/qtl2. See the rqtl-disc group for discussion about the original R/qtl, and rqtl-announce to receive only announcements of software updates about R/qtl and R/qtl2.

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jcb...@gmail.com, Karl Broman2

Jun 3

Allelic series number estimation

Consider the package TIMBR https://github.com/wesleycrouse/TIMBR See Crouse et al (2020) https://doi.

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Allelic series number estimation

Consider the package TIMBR https://github.com/wesleycrouse/TIMBR See Crouse et al (2020) https://doi.

Jun 3

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

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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 Broman2

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

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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

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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 Broman5

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

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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 Gatti5

Mar 27

modifying DO allele probabilities

So, the rounding operation needs values multiplied by 2 to round correctly. Then you could divide the

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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 Gatti2

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

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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 Broman2

Mar 13

Phenotype data set up

For the analysis of recombinant inbred lines, I prefer to focus on strain means, as for QTL mapping

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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 Broman2

12/13/24

plotGeno with cross2 data

There's not any facility for converting data from cross2 to cross1 format. And unfortunately

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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 Broman5

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

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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 Broman3

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

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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 Broman2

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

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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 Broman4

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

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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 Broman2

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/

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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 Gatti4

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

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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 Broman2

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

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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 Broman7

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

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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 Broman5

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

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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 Broman3

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,

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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

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QTL co-detection

Hello everyone, When analyzing the same trait in multiple environments, detecting a consistent and

6/6/24

Sam Mantel, Karl Broman3

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

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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 Gatti15

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

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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 Gatti11

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

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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 Broman9

5/17/24

invalid genotypes in cross

You can ignore the warning. The heterozygote genotypes will be treated as missing. To avoid the

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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 Broman9

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

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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

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 Broman2

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 <

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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 Broman4

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

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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

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

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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 Broman3

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. -

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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

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