Search

Clear search

Close search

Main menu

Google apps

R/qtl discussion

1–30 of 1302

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.

0 selected

Adrianna Jurek, Karl Broman6

Mar 21

Sex as an Interactive Covariate

What I meant, in doing it by hand, is something like the following: for(i in 1:1000) { tempx <-

unread,

Sex as an Interactive Covariate

What I meant, in doing it by hand, is something like the following: for(i in 1:1000) { tempx <-

Mar 21

Adrianna Jurek, Karl Broman7

Mar 18

F2 cross and pgm

Great! Thank you so much for your quick and helpful responses, I very much appreciate it. Adrianna On

unread,

F2 cross and pgm

Great! Thank you so much for your quick and helpful responses, I very much appreciate it. Adrianna On

Mar 18

Adrianna Jurek, Karl Broman3

Mar 17

X'X Matrix is Singular, X Chr issues

I do not seem to have the same issue running "hk" instead of "ehk". There are no

unread,

X'X Matrix is Singular, X Chr issues

I do not seem to have the same issue running "hk" instead of "ehk". There are no

Mar 17

N I, Karl Broman2

Feb 24

Confused about data types

I think it is likely fine to treat it as a continuous measurement. R/qtl doesn't have any special

unread,

Confused about data types

I think it is likely fine to treat it as a continuous measurement. R/qtl doesn't have any special

Feb 24

Jan 17

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

unread,

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 17

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:

unread,

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

12/28/24

make a genitic map from zero

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

unread,

make a genitic map from zero

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

12/28/24

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

unread,

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

11/14/24

Single marker analysis with R/qtl

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

unread,

Single marker analysis with R/qtl

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

11/14/24

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

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

8/22/24

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.

unread,

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.

8/22/24

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

unread,

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)

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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

unread,

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(

unread,

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

unread,

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

4/16/24

qtlDesign not available for newer versions of R

The qtlDesign package is again available at CRAN, https://cran.r-project.org/package=qtlDesign karl

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

4/16/24

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

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

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

unread,

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

unread,

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

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

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

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

3/18/24