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R/qtl2 discussion
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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
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to receive only announcements of software updates about R/qtl and R/qtl2.
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Mark Sfeir
, …
Karl Broman
4
Jul 29
Zooming in on plot_coefCC
Thank you both! How convenient. On Thursday, July 28, 2022 at 6:34:54 PM UTC-4 kbr...@gmail.com wrote
unread,
Zooming in on plot_coefCC
Thank you both! How convenient. On Thursday, July 28, 2022 at 6:34:54 PM UTC-4 kbr...@gmail.com wrote
Jul 29
Gabe Rangel
,
Karl Broman
2
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
unread,
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 Gatti
8
Jul 25
Dual peak for binary trait mapping
Thanks both, I really appreciate the help/insights. I've done some looking into the recombinants,
unread,
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 Gatti
4
Jul 21
Kinship in scan1snps
Hi both, Thanks for your suggestions. I tried running this with only 3 cores and the RAM usage was ~
unread,
Kinship in scan1snps
Hi both, Thanks for your suggestions. I tried running this with only 3 cores and the RAM usage was ~
Jul 21
Aravindh Nagarajan
,
Karl Broman
2
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=
unread,
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 Broman
3
Jul 12
MMnGM Genotype Cleaning
Yes, it makes sense that the different markers between arrays would make the cleaning more difficult
unread,
MMnGM Genotype Cleaning
Yes, it makes sense that the different markers between arrays would make the cleaning more difficult
Jul 12
123
,
Karl Broman
3
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
unread,
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 Broman
3
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:
unread,
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 Broman
2
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
unread,
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 Broman
2
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.
unread,
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
Mark Sfeir
,
Karl Broman
3
Jun 22
Normality assumptions in qtl2
Ok, thank you, let me process this... -Mark On Saturday, June 18, 2022 at 11:58:31 AM UTC-4 kbr...@
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Normality assumptions in qtl2
Ok, thank you, let me process this... -Mark On Saturday, June 18, 2022 at 11:58:31 AM UTC-4 kbr...@
Jun 22
Roshan Abeyratne
,
Karl Broman
3
Jun 12
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 <kbroman@gmail.com>
unread,
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 <kbroman@gmail.com>
Jun 12
Mark Sfeir
, …
Dan Gatti
6
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
unread,
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 Broman
3
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
unread,
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 Broman
9
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
unread,
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 Broman
2
Apr 14
QTL analysis on F3 single plants
Genotyping and phenotyping the F3 plants seems a perfectly reasonable strategy, though I don't
unread,
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 Skelly
6
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
unread,
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 Broman
2
Feb 18
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
unread,
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 18
Richard Radcliffe
,
Karl Broman
4
Feb 15
CC genotypes
Yes, I'm sure it can be done. karl On Tue, Feb 15, 2022 at 11:32 AM Richard Radcliffe <ra.
unread,
CC genotypes
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 Broman
7
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 Gatti
4
Jan 19
kinship matrix plot
Thank you so much for your answers. this individual had a very low quality genotyping (only 41
unread,
kinship matrix plot
Thank you so much for your answers. this individual had a very low quality genotyping (only 41
Jan 19
elsade...@gmail.com
,
Karl Broman
4
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
unread,
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 Broman
5
10/30/21
Genetic map
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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Genetic map
Hi Karl, Thank you so much! Regards, Denis пятница, 29 октября 2021 г. в 23:47:54 UTC+3, kbr...@gmail
10/30/21
Karl Broman
2
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://
unread,
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 Broman
5
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:
unread,
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 Broman
4
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
unread,
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 Broman
3
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
unread,
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 Broman
5
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
unread,
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
Karl Broman
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://
unread,
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 Broman
5
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:
unread,
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