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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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

shepher...@gmail.com, Karl Broman2

10/14/22

Remove redundant markers

There's a function findDupMarkers() for identifying markers with identical data. There's also

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Remove redundant markers

There's a function findDupMarkers() for identifying markers with identical data. There's also

10/14/22

Tiago Ribeiro, Karl Broman2

10/3/22

LOD score permutation too high?

Significance thresholds for two-dimensional scan can be large. They depend principally on genome size

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LOD score permutation too high?

Significance thresholds for two-dimensional scan can be large. They depend principally on genome size

10/3/22

Tiago Ribeiro, Karl Broman2

9/25/22

scantwo permutation - parallelization

You need to make sure that each run gets a different seed. What I do is use set.seed() with a large

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scantwo permutation - parallelization

You need to make sure that each run gets a different seed. What I do is use set.seed() with a large

9/25/22

laavanya rayaprolu, Karl Broman4

9/6/22

Missing phenotypes

They can be used as “NA”. You should get identical results. karl On Tuesday, September 6, 2022 at 3:

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Missing phenotypes

They can be used as “NA”. You should get identical results. karl On Tuesday, September 6, 2022 at 3:

9/6/22

David O'Donnell, Lipps, Sarah J2

8/4/22

Random sampling in R to obtain a p-value

Hi David, I am uncertain how to do this using r/qtl, but this can be done on the command line using

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Random sampling in R to obtain a p-value

Hi David, I am uncertain how to do this using r/qtl, but this can be done on the command line using

8/4/22

Tiago Ribeiro, Martin Ferris2

8/2/22

Karl will have to confirm, but c should influence the a* and k* estimates between pairs of markers. I

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Karl will have to confirm, but c should influence the a* and k* estimates between pairs of markers. I

8/2/22

David, … Lara13

7/21/22

mqmscan singular matrix

Thanks, I updated the package and re-ran checkAlleles() with markerlrt(). It returned that there are

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mqmscan singular matrix

Thanks, I updated the package and re-ran checkAlleles() with markerlrt(). It returned that there are

7/21/22

7/9/22

R/qtl version 1.52

A new version of R/qtl (1.52) has been released at its website (https://rqtl.org) and on CRAN.

unread,

R/qtl version 1.52

A new version of R/qtl (1.52) has been released at its website (https://rqtl.org) and on CRAN.

7/9/22

mukesh choudhary, Karl Broman4

7/1/22

Coding of the markers for SNP markers where parents have heterozygous condition?

R/qtl is developed for crosses between inbred lines, and can't handle heterozygosity in the

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Coding of the markers for SNP markers where parents have heterozygous condition?

R/qtl is developed for crosses between inbred lines, and can't handle heterozygosity in the

7/1/22

Jen, … mukesh choudhary9

6/30/22

dominant markers and formLinkageGroups()

Can you please help me with how the coding was fixed for dominant markers? I am struggling with my

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dominant markers and formLinkageGroups()

Can you please help me with how the coding was fixed for dominant markers? I am struggling with my

6/30/22

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