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R/qtl2 discussion
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This group is for discussion about the use of
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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 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
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 17
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
unread,
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 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 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
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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 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://
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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 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:
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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 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
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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 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://
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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 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:
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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 Radcliffe
5
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.
unread,
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 Boehm
5
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
unread,
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 Broman
3
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
unread,
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 Broman
3
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 Broman
6
3/16/21
Error in calling qtl2
Dear Karl, update.packages() worked for me. Thanks. Ganesh Prasad Ph. D. Scholar, Department of
unread,
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 Broman
5
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
unread,
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 Broman
3
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
unread,
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 Broman
3
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 Broman
10
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 Broman
4
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
unread,
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 Broman
4
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 Broman
2
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
unread,
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