R/qtl discussion

1–30 of 1251

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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Oluyinka Ilesanmi, Karl Broman3

Sep 5

Estimating genetic maps

Dear Dr Broman, Thank you for your response. The issue is that I cannot seem to find the markers that

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Estimating genetic maps

Dear Dr Broman, Thank you for your response. The issue is that I cannot seem to find the markers that

Sep 5

Ellen R, Karl Broman6

Aug 30

Thanks, I wasn't sure where to start so this is helpful. Appreciate the assistance. Ellen On

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Thanks, I wasn't sure where to start so this is helpful. Appreciate the assistance. Ellen On

Aug 30

Stephen Parris, Karl Broman3

Aug 24

effectplot variance

Thank you! On Thu, Aug 24, 2023 at 2:38 PM Karl Broman <kbr...@gmail.com> wrote: The

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effectplot variance

Thank you! On Thu, Aug 24, 2023 at 2:38 PM Karl Broman <kbr...@gmail.com> wrote: The

Aug 24

PAWANDEEP Singh, Karl Broman7

Aug 3

Interpreting interaction estimate from fitqtl

Got it! Thank you for explaining it. Pawandeep Singh On Thu, Aug 3, 2023, 00:10 Karl Broman <

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Interpreting interaction estimate from fitqtl

Got it! Thank you for explaining it. Pawandeep Singh On Thu, Aug 3, 2023, 00:10 Karl Broman <

Aug 3

Ellen R, Karl Broman4

Jul 16

summary of 2part model

No it just uses quantile() karl On Sunday, July 16, 2023 at 4:17:35 PM UTC-5 elris...@gmail.com wrote

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summary of 2part model

No it just uses quantile() karl On Sunday, July 16, 2023 at 4:17:35 PM UTC-5 elris...@gmail.com wrote

Jul 16

Anji Ballerini, … Jason Johns7

Jul 13

Negative LOD scores with scanone

Hi Karl, I would be happy to share the data with you but the problem is fixed. Thank you for your

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Negative LOD scores with scanone

Hi Karl, I would be happy to share the data with you but the problem is fixed. Thank you for your

Jul 13

Amir FARTASH, Karl Broman3

May 4

Interpret the values of Estimated effects derived from Multiple-QTL model results on a RIL Pop.

Thank you very much for your nice and fast response Best regards On Thu, May 4, 2023 at 8:48 PM Karl

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Interpret the values of Estimated effects derived from Multiple-QTL model results on a RIL Pop.

Thank you very much for your nice and fast response Best regards On Thu, May 4, 2023 at 8:48 PM Karl

May 4

Ellen McMullen, Karl Broman6

Apr 27

Error: cons memory exhausted

Yes the assumeCondIndep can also be used in permutations. And if you're using Haley-Knott

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Error: cons memory exhausted

Yes the assumeCondIndep can also be used in permutations. And if you're using Haley-Knott

Apr 27

Apr 18

R/qtl version 1.60

A new version of R/qtl (1.60) has been released at its website (https://rqtl.org) and on CRAN.

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R/qtl version 1.60

A new version of R/qtl (1.60) has been released at its website (https://rqtl.org) and on CRAN.

Apr 18

Lena Flörl, Karl Broman2

Mar 22

Bayes Credible Interval is zero or negative?

You apparently have a very sharp peak. I can't say whether it's real or fake. You might re-

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Bayes Credible Interval is zero or negative?

You apparently have a very sharp peak. I can't say whether it's real or fake. You might re-

Mar 22

Atoosa Samani, Karl Broman5

Mar 3

error using addint function for mqm

I was able to reproduce the problem with the `fake.f2` dataset. It seems that `addint()` is not

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error using addint function for mqm

I was able to reproduce the problem with the `fake.f2` dataset. It seems that `addint()` is not

Mar 3

Ellen R, Karl Broman2

Feb 27

Plot without x-axis ticks/labels

Unfortunately, there's limited control over that sort of thing. So you're best bet is to make

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Plot without x-axis ticks/labels

Unfortunately, there's limited control over that sort of thing. So you're best bet is to make

Feb 27

Lena Flörl, Karl Broman8

Feb 16

Filter for significant phenotypes

Hi Karl - thanks a lot! On Wednesday, 15 February 2023 at 19:01:40 UTC-8 Karl Broman wrote: Those are

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Filter for significant phenotypes

Hi Karl - thanks a lot! On Wednesday, 15 February 2023 at 19:01:40 UTC-8 Karl Broman wrote: Those are

Feb 16

Jason Johns, Karl Broman2

Feb 12

plotlodprofile without using refineqtl

I think you'll have to just do this “by hand”. Loop over positions on the chromosome, call

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plotlodprofile without using refineqtl

I think you'll have to just do this “by hand”. Loop over positions on the chromosome, call

Feb 12

Princia NAKOMBO, Karl Broman2

Feb 6

QTL analysis_distorsion segregation

I would not omit the heterozygotes, particularly as they are 25% of the data. I don't understand

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QTL analysis_distorsion segregation

I would not omit the heterozygotes, particularly as they are 25% of the data. I don't understand

Feb 6

Rohan Richard, … Martin Ferris5

Feb 3

Scantwo function output interpretation

I've found, to decrease the computational time, I can decrease my marker density to save on

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Scantwo function output interpretation

I've found, to decrease the computational time, I can decrease my marker density to save on

Feb 3

Thomas Blankers, Karl Broman3

Feb 1

fitqtl effect estimates for X chromosome

Thanks! Op donderdag 26 januari 2023 om 15:45:55 UTC+1 schreef kbr...@gmail.com: Unfortunately,

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fitqtl effect estimates for X chromosome

Thanks! Op donderdag 26 januari 2023 om 15:45:55 UTC+1 schreef kbr...@gmail.com: Unfortunately,

Feb 1

Lena Flörl, Karl Broman5

Jan 31

Multiple phenotypes: multivariate regression vs loop over single traits

Dear Karl, thanks a lot for the explanation - I'll have a closer look at the p-values then!

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Multiple phenotypes: multivariate regression vs loop over single traits

Dear Karl, thanks a lot for the explanation - I'll have a closer look at the p-values then!

Jan 31

Martin Ferris, Karl Broman2

Jan 27

conversion functions

No there isn't; sorry. karl On Friday, January 27, 2023 at 9:08:56 AM UTC-6 martin....@gmail.com

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conversion functions

No there isn't; sorry. karl On Friday, January 27, 2023 at 9:08:56 AM UTC-6 martin....@gmail.com

Jan 27

Princia NAKOMBO, Karl Broman3

Jan 20

Hello, i have 175 individuals and 941 markers princia Le lundi 16 janvier 2023 à 16:36:01 UTC+1, kbr.

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Hello, i have 175 individuals and 941 markers princia Le lundi 16 janvier 2023 à 16:36:01 UTC+1, kbr.

Jan 20

Arasi, Karl Broman2

Jan 18

determine the source that contributes the allele for particular QTL?

You can use the functions plotPXG() or effectplot() to plot the phenotype vs the genotype at a locus.

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determine the source that contributes the allele for particular QTL?

You can use the functions plotPXG() or effectplot() to plot the phenotype vs the genotype at a locus.

Jan 18

Jan 7

R/qtl version 1.58

A new version of R/qtl (1.58) has been released at its website (https://rqtl.org) and on CRAN.

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R/qtl version 1.58

A new version of R/qtl (1.58) has been released at its website (https://rqtl.org) and on CRAN.

Jan 7

12/1/22

R/qtl version 1.54

A new version of R/qtl (1.54) has been released at its website (https://rqtl.org) and on CRAN.

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R/qtl version 1.54

A new version of R/qtl (1.54) has been released at its website (https://rqtl.org) and on CRAN.

12/1/22

Tiago Ribeiro, Karl Broman2

11/29/22

Additive dominance model

R/qtl doesn't have any facility for additive or dominance models. And for RIL, it omits and

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Additive dominance model

R/qtl doesn't have any facility for additive or dominance models. And for RIL, it omits and

11/29/22

Etienne Dvorak, Karl Broman4

11/29/22

Markers at the wrong end of a linkage group

orderMarkers() uses a pretty simplistic method. I don't think it's worth thinking too hard

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Markers at the wrong end of a linkage group

orderMarkers() uses a pretty simplistic method. I don't think it's worth thinking too hard

11/29/22

Ellen Risemberg, Karl Broman3

11/8/22

perm.strata vs addcovar in scanoneperm

This makes sense, thanks! On Tuesday, November 1, 2022 at 10:16:39 AM UTC-4 kbr...@gmail.com wrote:

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perm.strata vs addcovar in scanoneperm

This makes sense, thanks! On Tuesday, November 1, 2022 at 10:16:39 AM UTC-4 kbr...@gmail.com wrote:

11/8/22

Princia NAKOMBO, Karl Broman9

11/3/22

Use of countXO or locateX0

You can start with physical distances, but it's maybe best to provide Mbp rather than bp

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Use of countXO or locateX0

You can start with physical distances, but it's maybe best to provide Mbp rather than bp

11/3/22

xu4...@gmail.com, Karl Broman3

11/2/22

function plot.pxg not found in version 1.52

Got it! Thanks! On Wednesday, November 2, 2022 at 1:16:00 PM UTC-5 kbr...@gmail.com wrote: It was

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function plot.pxg not found in version 1.52

Got it! Thanks! On Wednesday, November 2, 2022 at 1:16:00 PM UTC-5 kbr...@gmail.com wrote: It was

11/2/22

Tiago Ribeiro, Karl Broman3

10/28/22

Simulating genotype skew

It is an intercross (F12), I suspect that one of the two parental inbred strains might have produced

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Simulating genotype skew

It is an intercross (F12), I suspect that one of the two parental inbred strains might have produced

10/28/22

Ramesh Bhat, … Karl Broman510

10/15/22

Single marker analysis with R/qtl

No, there isn't. karl On Saturday, October 15, 2022 at 3:48:04 AM UTC-5 Ramesh Bhat wrote: Is

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Single marker analysis with R/qtl

No, there isn't. karl On Saturday, October 15, 2022 at 3:48:04 AM UTC-5 Ramesh Bhat wrote: Is

10/15/22

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