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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Helene Grindeland, Karl Broman2

Nov 19

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

Nov 19

Ramesh Bhat, … Karl Broman557

Nov 13

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

Nov 13

Lena Flörl, Karl Broman6

Nov 1

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

Nov 1

Siri B, Karl Broman3

Oct 17

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

Oct 17

Nathaniel Burner

Oct 16

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

Oct 16

Lena Flörl, Karl Broman3

Oct 2

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

Oct 2

Forest Hunt, Karl Broman2

Sep 23

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

Sep 23

Aug 21

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.

Aug 21

Muhammad Habib Widyawan, Karl Broman2

Aug 14

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

Aug 14

Lena Flörl, Karl Broman3

Jul 26

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)

Jul 26

HECTOR LOPEZ MORENO

Jun 18

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

Jun 18

May 30

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

May 30

Robert Mattera, Karl Broman4

May 19

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

May 19

PAWANDEEP Singh, Karl Broman5

May 14

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

May 14

Corin Stansfield, Karl Broman2

May 3

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

May 3

Maunveri, Karl Broman2

Apr 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(

Apr 24

Joshua Havill, Karl Broman2

Apr 18

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

Apr 18

Richard Merrill, Karl Broman4

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

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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

Apr 15

Maunveri, … Karl Broman5

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

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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

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

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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

Mar 23

Othmane Lamoumni, Karl Broman3

Mar 21

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

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

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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

Mar 20

Eric González, Karl Broman2

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

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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

Mar 18

Tami Hildahl, … Karl Broman5

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

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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

Mar 15

Nathaniel Burner, Karl Broman2

Mar 11

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

Mar 11

Nathaniel Burner2

Mar 8

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

Mar 8

Nathaniel Burner, Karl Broman2

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 Broman2

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,

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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 Broman5

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 Broman2

Feb 9

Rationale behind convert2riself genotype conversion

Just trying to guess at which are the correct genotype labels. Most commonly, the data initially get

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Rationale behind convert2riself genotype conversion

Just trying to guess at which are the correct genotype labels. Most commonly, the data initially get

Feb 9

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