R/qtl2 discussion

1–30 of 180

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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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

Akinlade Oluwaseun Johnson, Karl Broman5

10/25/21

Using ATGC genotype format

Thank you so much, Karl. On Wednesday, October 20, 2021 at 7:19:34 AM UTC+10 kbr...@gmail.com wrote:

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Using ATGC genotype format

Thank you so much, Karl. On Wednesday, October 20, 2021 at 7:19:34 AM UTC+10 kbr...@gmail.com wrote:

10/25/21

Dan Skelly, Karl Broman4

10/7/21

Using DOF1 cross type for CCRIX x B6

I just implemented an "hsf1" cross type, like the "dof1" but assuming a more

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Using DOF1 cross type for CCRIX x B6

I just implemented an "hsf1" cross type, like the "dof1" but assuming a more

10/7/21

Richard Radcliffe, Karl Broman3

10/5/21

CI issue with find_peaks

That did the trick. Thanks and thanks for the speedy response. -Richard On Tuesday, October 5, 2021

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CI issue with find_peaks

That did the trick. Thanks and thanks for the speedy response. -Richard On Tuesday, October 5, 2021

10/5/21

elsade...@gmail.com, … Karl Broman5

9/21/21

how to read in saved scan1 output

The row names in a scan1 object are critical. They need to contain the marker names and are used to

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how to read in saved scan1 output

The row names in a scan1 object are critical. They need to contain the marker names and are used to

9/21/21

9/13/21

Tutorial on identifying sample-mixups in DO mice

I just posted a new tutorial, on identifying sample mix-ups in Diversity Outbred mice: https://

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Tutorial on identifying sample-mixups in DO mice

I just posted a new tutorial, on identifying sample mix-ups in Diversity Outbred mice: https://

9/13/21

CJ Harbort, Karl Broman5

8/11/21

Converting Allele probs to genotype probs?

Perfect! Thanks a lot CJ On Tue, Aug 10, 2021 at 5:49 PM Karl Broman <kbroman@gmail.com> wrote:

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Converting Allele probs to genotype probs?

Perfect! Thanks a lot CJ On Tue, Aug 10, 2021 at 5:49 PM Karl Broman <kbroman@gmail.com> wrote:

8/11/21

Harry C., … Richard Radcliffe5

6/9/21

Founder effects (coef) help

Aha. That makes sense. I'll poke around a bit and see if that's the case for all the NAs.

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Founder effects (coef) help

Aha. That makes sense. I'll poke around a bit and see if that's the case for all the NAs.

6/9/21

Conor Simpson, Fred Boehm5

4/26/21

Use of qtl2pleio for simple bi-parental

Hi Fred, No worries I really appreciate the advice. This is not a major part of my PhD and has taken

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Use of qtl2pleio for simple bi-parental

Hi Fred, No worries I really appreciate the advice. This is not a major part of my PhD and has taken

4/26/21

Zachary Tatom, Karl Broman3

4/2/21

Permutation Analysis for SNP Significance?

Thanks! If there's any way to aid in its implementation, please let me know. On Thursday, April 1

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Permutation Analysis for SNP Significance?

Thanks! If there's any way to aid in its implementation, please let me know. On Thursday, April 1

4/2/21

Dan Zhou, Karl Broman3

3/20/21

A quick question about the alelles.

Thanks a lot! Dan On Sat, Mar 20, 2021 at 3:38 PM Karl Broman <kbroman@gmail.com> wrote: The

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A quick question about the alelles.

Thanks a lot! Dan On Sat, Mar 20, 2021 at 3:38 PM Karl Broman <kbroman@gmail.com> wrote: The

3/20/21

Ganesh Prasad, Karl Broman6

3/16/21

Error in calling qtl2

Dear Karl, update.packages() worked for me. Thanks. Ganesh Prasad Ph. D. Scholar, Department of

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Error in calling qtl2

Dear Karl, update.packages() worked for me. Thanks. Ganesh Prasad Ph. D. Scholar, Department of

3/16/21

Aravindh Nagarajan, Karl Broman5

3/11/21

CC mice - adding sex as a covariate and CC078

"object 'local_file' not found" would be related to line 30. The object local_file

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CC mice - adding sex as a covariate and CC078

"object 'local_file' not found" would be related to line 30. The object local_file

3/11/21

Richard Radcliffe, Karl Broman3

3/10/21

GigaMUGA consesnus SNPs

Thanks for the info. I'm working with the HS/Npt mice which have a different but overlapping set

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GigaMUGA consesnus SNPs

Thanks for the info. I'm working with the HS/Npt mice which have a different but overlapping set

3/10/21

Randall Marshall, Karl Broman3

3/9/21

finalreport.txt + finalreportmatrixforward.txt file handling

It's that finalreport.txt data format but the typical X&Y columns/rows transposed... so we

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finalreport.txt + finalreportmatrixforward.txt file handling

It's that finalreport.txt data format but the typical X&Y columns/rows transposed... so we

3/9/21

Aravindh Nagarajan, Karl Broman10

3/5/21

CC F2 Cross - gmap required? plots look different? QTL effects are off

That makes sense. Thank you. Aravindh Nagarajan \ AH-rah-'vind\ Genetics Ph.D. Candidate |

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CC F2 Cross - gmap required? plots look different? QTL effects are off

That makes sense. Thank you. Aravindh Nagarajan \ AH-rah-'vind\ Genetics Ph.D. Candidate |

3/5/21

kidd...@gmail.com, Karl Broman4

3/4/21

standard error for heritability estimates

Hello Karl, Thanks a lot for the quick answer and putting together code. Will run it on some data and

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standard error for heritability estimates

Hello Karl, Thanks a lot for the quick answer and putting together code. Will run it on some data and

3/4/21

a b, … Karl Broman4

2/26/21

variance explained

I've not done anything further on this. You can see the changes in the package in the NEWS file,

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variance explained

I've not done anything further on this. You can see the changes in the package in the NEWS file,

2/26/21

Sam Mantel, Karl Broman2

2/18/21

Most appropriate cross type?

We don't really have a cross type that fits. There's nothing in R/qtl2 for RIX populations. I

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Most appropriate cross type?

We don't really have a cross type that fits. There's nothing in R/qtl2 for RIX populations. I

2/18/21

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