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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elsade...@gmail.com, Karl Broman2

9:04 AM

how to read in saved scan1 output

Try class(myobject) <- c("scan1", "matrix") karl On Thursday, September 16,

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how to read in saved scan1 output

Try class(myobject) <- c("scan1", "matrix") karl On Thursday, September 16,

9:04 AM

Sep 13

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://

Sep 13

CJ Harbort, Karl Broman5

Aug 11

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:

Aug 11

Harry C., … Richard Radcliffe5

Jun 9

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.

Jun 9

Conor Simpson, Fred Boehm5

Apr 26

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

Apr 26

Zachary Tatom, Karl Broman3

Apr 2

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

Apr 2

Dan Zhou, Karl Broman3

Mar 20

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

Mar 20

Ganesh Prasad, Karl Broman6

Mar 16

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

Mar 16

Aravindh Nagarajan, Karl Broman5

Mar 11

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

Mar 11

Richard Radcliffe, Karl Broman3

Mar 10

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

Mar 10

Randall Marshall, Karl Broman3

Mar 9

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

Mar 9

Aravindh Nagarajan, Karl Broman10

Mar 5

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 |

Mar 5

kidd...@gmail.com, Karl Broman4

Mar 4

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

Mar 4

a b, … Karl Broman4

Feb 26

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,

Feb 26

Sam Mantel, Karl Broman2

Feb 18

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

Feb 18

Richard Radcliffe, Karl Broman3

Feb 18

zip_datafiles() not doing anything

Windows 10 Rstudio 1.4.1103 R 4.0.3 qtl2 0.24 The quiet=FALSE did not produce any messages or any

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zip_datafiles() not doing anything

Windows 10 Rstudio 1.4.1103 R 4.0.3 qtl2 0.24 The quiet=FALSE did not produce any messages or any

Feb 18

CJ Yang, Karl Broman3

Jan 18

constructing genetic map from 16-founder MAGIC

Hi Karl, Cool, I will give est_map() a try then. Sorry for the confusing statement. What I meant by

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constructing genetic map from 16-founder MAGIC

Hi Karl, Cool, I will give est_map() a try then. Sorry for the confusing statement. What I meant by

Jan 18

李凯, Karl Broman9

Jan 16

I couldn't read the yaml file

ok thank you very much! Sorry for disturbing! Karl Broman <kbroman@gmail.com> 于2021年1月16日周六下午8

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I couldn't read the yaml file

ok thank you very much! Sorry for disturbing! Karl Broman <kbroman@gmail.com> 于2021年1月16日周六下午8

Jan 16

12/18/20

R/qtl2 version 0.24

Just posted a new version of R/qtl2 to CRAN. The windows and Mac binaries should show up in a few

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R/qtl2 version 0.24

Just posted a new version of R/qtl2 to CRAN. The windows and Mac binaries should show up in a few

12/18/20

Stephen Deslauriers, Karl Broman3

12/14/20

Additive genetic variance and environmental variance analysis

Thanks for the feedback! On Friday, December 11, 2020 at 11:46:24 AM UTC-6 kbr...@gmail.com wrote:

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Additive genetic variance and environmental variance analysis

Thanks for the feedback! On Friday, December 11, 2020 at 11:46:24 AM UTC-6 kbr...@gmail.com wrote:

12/14/20

Flerpan, Karl Broman2

11/30/20

scan1; max_batch

As it says in the help file for scan1(), "max_batch indicates the maximum number of phenotypes

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scan1; max_batch

As it says in the help file for scan1(), "max_batch indicates the maximum number of phenotypes

11/30/20

changs...@gmail.com, Karl Broman5

11/25/20

some functions didn't work in my dataset

Thank you. Wish you a good day! Pengfei Wang 在2020年11月25日星期三 UTC+8 下午10:18:09<kbr...@gmail.com>

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some functions didn't work in my dataset

Thank you. Wish you a good day! Pengfei Wang 在2020年11月25日星期三 UTC+8 下午10:18:09<kbr...@gmail.com>

11/25/20

Bowen Jones, Karl Broman6

11/24/20

Imputation with qtl2

Changing the cross type indeed solved the three value problem, thank you! Bowen On Tuesday, November

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Imputation with qtl2

Changing the cross type indeed solved the three value problem, thank you! Bowen On Tuesday, November

11/24/20

katz...@gmail.com, Karl Broman6

11/4/20

Thanks, Karl. On Wed, Nov 4, 2020 at 7:09 PM Karl Broman <kbroman@gmail.com> wrote: The source

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Thanks, Karl. On Wed, Nov 4, 2020 at 7:09 PM Karl Broman <kbroman@gmail.com> wrote: The source

11/4/20

Randall Marshall, Karl Broman5

10/22/20

Header-only chromosome files when processing Geneseek

Good advice - you know what it was, it didn't like the header on the GM_allelecodes.csv file,

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Header-only chromosome files when processing Geneseek

Good advice - you know what it was, it didn't like the header on the GM_allelecodes.csv file,

10/22/20

kidd...@gmail.com, Karl Broman2

10/12/20

We treat the SNP probabilities as a special case of the general multi-allelic probabilities. And SNP

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We treat the SNP probabilities as a special case of the general multi-allelic probabilities. And SNP

10/12/20

annae...@outlook.com, Karl Broman3

10/11/20

pheno has no name error

Thanks Karl! All sorted! On Sunday, October 11, 2020 at 4:37:12 PM UTC+11 kbr...@gmail.com wrote: The

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pheno has no name error

Thanks Karl! All sorted! On Sunday, October 11, 2020 at 4:37:12 PM UTC+11 kbr...@gmail.com wrote: The

10/11/20

Juan Camilo Sánchez Arcila, Karl Broman2

9/1/20

Colors in SNP plot

The genes colors are arbitrary. That part of the plot is made by plot_genes(). The argument colors: “

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Colors in SNP plot

The genes colors are arbitrary. That part of the plot is made by plot_genes(). The argument colors: “

9/1/20

Ramesh Bhat, Karl Broman12

8/20/20

QTL analysis with MAGIC population

Dear Dr. Karl, Can we get the effects and gene annotations for the SNPs using R/qtl2 especially for

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QTL analysis with MAGIC population

Dear Dr. Karl, Can we get the effects and gene annotations for the SNPs using R/qtl2 especially for

8/20/20

Senthil Thillainadesan, Karl Broman3

8/13/20

Parallelization of scan1snps (Error: k_loco not found)

Sorry! I should have included the code to begin with. This works fine (using 1 core to do whole

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Parallelization of scan1snps (Error: k_loco not found)

Sorry! I should have included the code to begin with. This works fine (using 1 core to do whole

8/13/20

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