R/qtl2 discussion

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This group is for discussion about the use of R/qtl2. See the rqtl-disc group for discussion about the original R/qtl, and rqtl-announce to receive only announcements of software updates about R/qtl and R/qtl2.

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Dec 2

R/qtl2 version 0.30

A new version of R/qtl2 (version 0.30) has been released on CRAN. Windows and Mac binaries will be

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R/qtl2 version 0.30

A new version of R/qtl2 (version 0.30) has been released on CRAN. Windows and Mac binaries will be

Dec 2

Mark Sfeir, Dan Gatti5

Nov 11

Permutation test LOD thresholds and Bonferroni correction

I'm still planning to look at the Benjamini-Hochberg and q-value approaches to assessing

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Permutation test LOD thresholds and Bonferroni correction

I'm still planning to look at the Benjamini-Hochberg and q-value approaches to assessing

Nov 11

Dan Gatti, Karl Broman2

Oct 25

F3 ail input produces choppy haplotype reconstructions

Hi, Dan, For two-way crosses like AIL, the founder genotypes are not used, but instead you need to re

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F3 ail input produces choppy haplotype reconstructions

Hi, Dan, For two-way crosses like AIL, the founder genotypes are not used, but instead you need to re

Oct 25

Mark Sfeir, Karl Broman6

Oct 13

Normality assumptions in qtl2

Thank you, but again I'm not going to choose transformations based on LOD score, I was only

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Normality assumptions in qtl2

Thank you, but again I'm not going to choose transformations based on LOD score, I was only

Oct 13

William Pu, Karl Broman9

Sep 30

DO cross questions

I've looked more closely at the two main genotype diagnostic functions for the DOF1: -

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DO cross questions

I've looked more closely at the two main genotype diagnostic functions for the DOF1: -

Sep 30

William Pu, … Mark Sfeir5

Sep 14

Phenotype that is not normally distributed

Thanks, Dan! I wondered if normal trait distribution was a common proxy for normal distribution of

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Phenotype that is not normally distributed

Thanks, Dan! I wondered if normal trait distribution was a common proxy for normal distribution of

Sep 14

Mark Sfeir, … Karl Broman7

Sep 6

Zooming in on plot_coefCC

That makes sense. Thank you! On Fri, Sep 2, 2022 at 4:37 PM Karl Broman <kbr...@gmail.com>

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Zooming in on plot_coefCC

That makes sense. Thank you! On Fri, Sep 2, 2022 at 4:37 PM Karl Broman <kbr...@gmail.com>

Sep 6

Alanna Carey, … Dan Gatti4

Aug 16

Trouble with Omissions of Individuals

Thank you both for such a fast response. I found some samples that were altered between pheno and

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Trouble with Omissions of Individuals

Thank you both for such a fast response. I found some samples that were altered between pheno and

Aug 16

Gabe Rangel, Karl Broman2

Jul 27

Trouble with scan1snps in haploid cross

I think the problem is that the SNP database, or the query function, needs to be revised to include

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Trouble with scan1snps in haploid cross

I think the problem is that the SNP database, or the query function, needs to be revised to include

Jul 27

Maggie Johansen, … Dan Gatti8

Jul 25

Dual peak for binary trait mapping

Thanks both, I really appreciate the help/insights. I've done some looking into the recombinants,

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Dual peak for binary trait mapping

Thanks both, I really appreciate the help/insights. I've done some looking into the recombinants,

Jul 25

Harry C., … Dan Gatti4

Jul 20

Kinship in scan1snps

Hi both, Thanks for your suggestions. I tried running this with only 3 cores and the RAM usage was ~

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Kinship in scan1snps

Hi both, Thanks for your suggestions. I tried running this with only 3 cores and the RAM usage was ~

Jul 20

Aravindh Nagarajan, Karl Broman2

Jul 20

Is it possible to run a two part model for Scan1?

It's not built in, but you can do a scan with a binary trait model, for a new trait defined by z=

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Is it possible to run a two part model for Scan1?

It's not built in, but you can do a scan with a binary trait model, for a new trait defined by z=

Jul 20

krij...@ucdavis.edu, Karl Broman3

Jul 11

MMnGM Genotype Cleaning

Yes, it makes sense that the different markers between arrays would make the cleaning more difficult

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MMnGM Genotype Cleaning

Yes, it makes sense that the different markers between arrays would make the cleaning more difficult

Jul 11

123, Karl Broman3

Jul 11

Can I used R/qtl2 with in-house generated mouse line with 4 parental strains?

Prof. Broman, thank you for your quick reply. Indeed, conversion from .bed/bim/fam is likely to be a

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Can I used R/qtl2 with in-house generated mouse line with 4 parental strains?

Prof. Broman, thank you for your quick reply. Indeed, conversion from .bed/bim/fam is likely to be a

Jul 11

Naveen Kumar, Karl Broman3

Jul 5

Does R/qtl works best for polyploid species like peanut (allotetraploid)

Dear Karl, Thanks for the reply. On Tuesday, July 5, 2022 at 2:44:16 PM UTC-4 kbr...@gmail.com wrote:

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Does R/qtl works best for polyploid species like peanut (allotetraploid)

Dear Karl, Thanks for the reply. On Tuesday, July 5, 2022 at 2:44:16 PM UTC-4 kbr...@gmail.com wrote:

Jul 5

Jacky S, Karl Broman2

Jun 30

Including kinship in binary mapping?

It turns out to be more complicated than it seems. I don't have a solution at this point. karl On

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Including kinship in binary mapping?

It turns out to be more complicated than it seems. I don't have a solution at this point. karl On

Jun 30

Mark Sfeir, Karl Broman2

Jun 29

Subsetting an existing cross2 object for select sample id's

There's a function subset.cross2 for subsetting cross2 objects by individuals and/or chromosomes.

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Subsetting an existing cross2 object for select sample id's

There's a function subset.cross2 for subsetting cross2 objects by individuals and/or chromosomes.

Jun 29

Roshan Abeyratne, Karl Broman3

Jun 11

Converting a read_cross2 object to read_cross

Thank you Karl. Sent from my iPhone On Jun 6, 2022, at 9:40 PM, Karl Broman <kbr...@gmail.com>

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Converting a read_cross2 object to read_cross

Thank you Karl. Sent from my iPhone On Jun 6, 2022, at 9:40 PM, Karl Broman <kbr...@gmail.com>

Jun 11

Mark Sfeir, … Dan Gatti6

May 12

DO mice, cross info, and "ngen" question

That is very interesting! Thanks for this, too, I do think it could be interesting how meiotic

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DO mice, cross info, and "ngen" question

That is very interesting! Thanks for this, too, I do think it could be interesting how meiotic

May 12

Mark Sfeir, Karl Broman3

May 11

qtl2 user guide genome-wide single-QTL scan DOex example error

That's good to know, and I am on Windows 10 Enterprise (64-bit OS, x64-based processor), using R

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qtl2 user guide genome-wide single-QTL scan DOex example error

That's good to know, and I am on Windows 10 Enterprise (64-bit OS, x64-based processor), using R

May 11

Mark Sfeir, Karl Broman9

Apr 28

Example cc_variants.sqlite dataset trouble

It looks like using mode = 'wb', the download worked as intended! I'm not sure if the

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Example cc_variants.sqlite dataset trouble

It looks like using mode = 'wb', the download worked as intended! I'm not sure if the

Apr 28

Itay, Karl Broman2

Apr 14

QTL analysis on F3 single plants

Genotyping and phenotyping the F3 plants seems a perfectly reasonable strategy, though I don't

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QTL analysis on F3 single plants

Genotyping and phenotyping the F3 plants seems a perfectly reasonable strategy, though I don't

Apr 14

Richard Baker, … Daniel A Skelly6

Mar 10

calc_genoprob for CC's

Thank you all for the advice and for pointing me to the available resources, especially Table S1 of

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calc_genoprob for CC's

Thank you all for the advice and for pointing me to the available resources, especially Table S1 of

Mar 10

段绍伟, Karl Broman2

Feb 17

SNP association in single QTL between SNP and phenotype of a soybean bi-parental RIL

Start by looking at the user guide, https://kbroman.org/qtl2/assets/vignettes/user_guide.html There

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SNP association in single QTL between SNP and phenotype of a soybean bi-parental RIL

Start by looking at the user guide, https://kbroman.org/qtl2/assets/vignettes/user_guide.html There

Feb 17

Richard Radcliffe, Karl Broman4

Feb 15

Yes, I'm sure it can be done. karl On Tue, Feb 15, 2022 at 11:32 AM Richard Radcliffe <ra.

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Yes, I'm sure it can be done. karl On Tue, Feb 15, 2022 at 11:32 AM Richard Radcliffe <ra.

Feb 15

Bora Kim, Karl Broman7

Feb 14

Can I use already existed probability data into qtl2

'interp_map' works perfectly : ) Thank you Karl for all your guidance. Have a good day! On

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Can I use already existed probability data into qtl2

'interp_map' works perfectly : ) Thank you Karl for all your guidance. Have a good day! On

Feb 14

Atoosa Samani, … Dan Gatti4

Jan 18

kinship matrix plot

Thank you so much for your answers. this individual had a very low quality genotyping (only 41

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kinship matrix plot

Thank you so much for your answers. this individual had a very low quality genotyping (only 41

Jan 18

elsade...@gmail.com, Karl Broman4

11/29/21

using snps in known gene as covariate

Since it's an 8-way MAGIC population, there are 8 possible alleles at the locus. You include

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using snps in known gene as covariate

Since it's an 8-way MAGIC population, there are 8 possible alleles at the locus. You include

11/29/21

Denis, Karl Broman5

10/30/21

Hi Karl, Thank you so much! Regards, Denis пятница, 29 октября 2021 г. в 23:47:54 UTC+3, kbr...@gmail

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Hi Karl, Thank you so much! Regards, Denis пятница, 29 октября 2021 г. в 23:47:54 UTC+3, kbr...@gmail

10/30/21

10/25/21

R/qtl2 version 0.28

The updated R/qtl2 package seems to need the latest version of the Rcpp package (1.0.7). See https://

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R/qtl2 version 0.28

The updated R/qtl2 package seems to need the latest version of the Rcpp package (1.0.7). See https://

10/25/21

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