R/qtl discussion

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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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Jan 16

Confused about scanone and scantwo with different results

I have an F1 population with ~250 grape individuals which I am testing for the presence of color

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Confused about scanone and scantwo with different results

I have an F1 population with ~250 grape individuals which I am testing for the presence of color

Jan 16

Meiling Wong, Karl Broman5

Jan 9

Interpreting p-values and LOD scores from fitqtl output.

Thank you so much Karl! On Wed, Jan 8, 2025 at 11:59 AM Karl Broman <kbr...@gmail.com> wrote:

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Interpreting p-values and LOD scores from fitqtl output.

Thank you so much Karl! On Wed, Jan 8, 2025 at 11:59 AM Karl Broman <kbr...@gmail.com> wrote:

Jan 9

Luigi Faino, … Samuel Wang8

12/27/24

make a genitic map from zero

Dear L: What methods were used to generate the genotype data? If the genotype data were generated

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make a genitic map from zero

Dear L: What methods were used to generate the genotype data? If the genotype data were generated

12/27/24

Helene Grindeland, Karl Broman2

11/19/24

Mapping of a qualitative trait

Generally, there's no inherent problem, in QTL mapping, with using very dense markers, as the

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Mapping of a qualitative trait

Generally, there's no inherent problem, in QTL mapping, with using very dense markers, as the

11/19/24

Ramesh Bhat, … Karl Broman557

11/13/24

Single marker analysis with R/qtl

One approach would be to change the chromosome IDs in the input data file. Alternatively, you change

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Single marker analysis with R/qtl

One approach would be to change the chromosome IDs in the input data file. Alternatively, you change

11/13/24

Lena Flörl, Karl Broman6

11/1/24

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

11/1/24

Siri B, Karl Broman3

10/17/24

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

10/17/24

Nathaniel Burner

10/16/24

MQM fixed residual variance

Hi Karl, I am having trouble understanding how MQM fixes residual error to that of the full model as

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MQM fixed residual variance

Hi Karl, I am having trouble understanding how MQM fixes residual error to that of the full model as

10/16/24

Lena Flörl, Karl Broman3

10/2/24

QTLs at markers with high entropy / variance

In regions with low entropy and low variance, you have little genotype information and so low power

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QTLs at markers with high entropy / variance

In regions with low entropy and low variance, you have little genotype information and so low power

10/2/24

Forest Hunt, Karl Broman2

9/23/24

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

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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

9/23/24

8/21/24

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.

8/21/24

Muhammad Habib Widyawan, Karl Broman2

8/14/24

PVE more than 100%

The PVE estimates provided by fitqtl is just a transformation of the LOD score, and only account for

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PVE more than 100%

The PVE estimates provided by fitqtl is just a transformation of the LOD score, and only account for

8/14/24

Lena Flörl, Karl Broman3

7/26/24

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)

7/26/24

HECTOR LOPEZ MORENO

6/18/24

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

6/18/24

5/30/24

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

5/30/24

Robert Mattera, Karl Broman4

5/19/24

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

5/19/24

PAWANDEEP Singh, Karl Broman5

5/14/24

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

5/14/24

Corin Stansfield, Karl Broman2

5/3/24

The results from fitqtl are not more sophisticated than the formula you cite. In fact, we just use

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The results from fitqtl are not more sophisticated than the formula you cite. In fact, we just use

5/3/24

Maunveri, Karl Broman2

4/24/24

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(

4/24/24

Joshua Havill, Karl Broman2

4/18/24

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

4/18/24

Richard Merrill, Karl Broman4

4/15/24

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

4/15/24

Maunveri, … Karl Broman5

4/8/24

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

4/8/24

Othmane Lamoumni

3/23/24

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

3/23/24

Othmane Lamoumni, Karl Broman3

3/21/24

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

3/21/24

edb...@gmail.com

3/20/24

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

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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

3/20/24

Eric González, Karl Broman2

3/18/24

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

3/18/24

Tami Hildahl, … Karl Broman5

3/15/24

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

3/15/24

Nathaniel Burner, Karl Broman2

3/11/24

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

3/11/24

Nathaniel Burner2

3/8/24

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

3/8/24

Nathaniel Burner, Karl Broman2

3/7/24

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

3/7/24

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