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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Fernando Andrade, Karl Broman7

Jul 3

question on kinship correction and model comparison

Thank you! Em quarta-feira, 3 de julho de 2024 às 12:38:38 UTC-3, Karl Broman escreveu: If you leave

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question on kinship correction and model comparison

Thank you! Em quarta-feira, 3 de julho de 2024 às 12:38:38 UTC-3, Karl Broman escreveu: If you leave

Jul 3

Chevreau Julien, Karl Broman5

Jul 2

Chromosomes on physical and genetic maps

Right, ok. As I aligned the reads and used this information to infer the linkage groups, marker order

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Chromosomes on physical and genetic maps

Right, ok. As I aligned the reads and used this information to infer the linkage groups, marker order

Jul 2

Saikat Bandyopadhyay, Karl Broman3

Jul 1

Best way to extract scan data for a specific genomic range

Oops in the line calling scan1(), it should have iron$pheno in place of pheno out <- scan1(probs,

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Best way to extract scan data for a specific genomic range

Oops in the line calling scan1(), it should have iron$pheno in place of pheno out <- scan1(probs,

Jul 1

Othmane Lamoumni

Jun 6

QTL co-detection

Hello everyone, When analyzing the same trait in multiple environments, detecting a consistent and

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QTL co-detection

Hello everyone, When analyzing the same trait in multiple environments, detecting a consistent and

Jun 6

Sam Mantel, Karl Broman3

Jun 5

High LOD scores across across the entire linkage map

I think the genotypes are confounded with cross, and so I would include cross covariate indicators in

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High LOD scores across across the entire linkage map

I think the genotypes are confounded with cross, and so I would include cross covariate indicators in

Jun 5

Karl Broman, … Dan Gatti15

May 29

R/qtl2 version 0.22

No. karl On Wednesday, May 29, 2024 at 6:11:56 AM UTC-5 Ramesh Bhat wrote: Yes, you are right. Is

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R/qtl2 version 0.22

No. karl On Wednesday, May 29, 2024 at 6:11:56 AM UTC-5 Ramesh Bhat wrote: Yes, you are right. Is

May 29

lehong...@gmail.com, … Dan Gatti11

May 24

Interaction in SNP association scan

Karl answered your question about scan1_blup(). eQTL mapping is largely the same as mapping a few

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Interaction in SNP association scan

Karl answered your question about scan1_blup(). eQTL mapping is largely the same as mapping a few

May 24

Madi Shoken, Karl Broman9

May 17

invalid genotypes in cross

You can ignore the warning. The heterozygote genotypes will be treated as missing. To avoid the

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invalid genotypes in cross

You can ignore the warning. The heterozygote genotypes will be treated as missing. To avoid the

May 17

Jennifer Jacob, … Karl Broman9

May 13

Error in convert_sex...

I have an FVB in there, so that is where the issue probably lies. As a non-DO, what is the best way

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Error in convert_sex...

I have an FVB in there, so that is where the issue probably lies. As a non-DO, what is the best way

May 13

May 13

R/qtl2 version 0.36

A new version of R/qtl2 (version 0.36) has been released on CRAN. Windows and Mac binaries will be

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R/qtl2 version 0.36

A new version of R/qtl2 (version 0.36) has been released on CRAN. Windows and Mac binaries will be

May 13

Madi Shoken, Karl Broman2

May 13

Markers with distorted segregation

calc_geno_freq() and calc_raw_geno_freq(). karl On Mon, May 13, 2024 at 2:55 AM Madi Shoken <

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Markers with distorted segregation

calc_geno_freq() and calc_raw_geno_freq(). karl On Mon, May 13, 2024 at 2:55 AM Madi Shoken <

May 13

Madi Shoken, Karl Broman4

May 4

Genetic map construction

Cross type is wheat RILs at F7 and the data is its genetic map. Thanks for the link, just found and

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Genetic map construction

Cross type is wheat RILs at F7 and the data is its genetic map. Thanks for the link, just found and

May 4

Apr 16

RE: [EXTERNAL][WARNING: ATTACHMENT UNSCANNED][Rqtl2-disc] "write_control_file"

If you look closely at the error message, you'll see that you have a double path in there. I can

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RE: [EXTERNAL][WARNING: ATTACHMENT UNSCANNED][Rqtl2-disc] "write_control_file"

If you look closely at the error message, you'll see that you have a double path in there. I can

Apr 16

Benjamin Van Raalte, Karl Broman3

Apr 8

R/qtlDesign new implementation with R/qtl2

Karl, Thanks so much for the quick reply. I'll go ahead and use "R/qtlDesign" then. -

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R/qtlDesign new implementation with R/qtl2

Karl, Thanks so much for the quick reply. I'll go ahead and use "R/qtlDesign" then. -

Apr 8

David Gopaulchan, Karl Broman2

Apr 4

QTL analysis on multi-parent mapping populations

R/qtl2 is not the appropriate tool for the analysis of these data. It's designed for crosses with

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QTL analysis on multi-parent mapping populations

R/qtl2 is not the appropriate tool for the analysis of these data. It's designed for crosses with

Apr 4

Billy Jiang, … Dan Gatti7

Apr 2

cleaning genptype/allele probability prior to scan1

I don't think so. The situation should be better in earlier generations. I tried the counting

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cleaning genptype/allele probability prior to scan1

I don't think so. The situation should be better in earlier generations. I tried the counting

Apr 2

Jonathan Berlingeri, Karl Broman2

Mar 21

Test usefulness of adding kinship; Can one run permutation on independent chromosomes

1. I don't have a way to assess model fit. If the differences are nominal, then in my mind

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Test usefulness of adding kinship; Can one run permutation on independent chromosomes

1. I don't have a way to assess model fit. If the differences are nominal, then in my mind

Mar 21

Kareem Midlej, Karl Broman2

Mar 4

find_peaks function significance 0.9 and 0.95

I would use something like summary(operm, alpha=0.05) to define the threshold to use in find_peaks,

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find_peaks function significance 0.9 and 0.95

I would use something like summary(operm, alpha=0.05) to define the threshold to use in find_peaks,

Mar 4

Saikat Bandyopadhyay, Karl Broman2

Feb 29

Performing co-localization with the QTL2 scan1snp() outputs

To calculate MAF, you could either use the allele frequencies in the founder lines, or use the allele

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Performing co-localization with the QTL2 scan1snp() outputs

To calculate MAF, you could either use the allele frequencies in the founder lines, or use the allele

Feb 29

venkat rami reddy, Karl Broman2

Feb 29

selection of the window for searching candidate genes

The usual methods for defining a QTL interval are 1.5-LOD support intervals (the function lod_int),

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selection of the window for searching candidate genes

The usual methods for defining a QTL interval are 1.5-LOD support intervals (the function lod_int),

Feb 29

Zachary Tatom, … Karl Broman4

Feb 26

SNP Association p-values

Thank you for your reply. I'm aware of the permutation function for overall QTL p-values (the

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SNP Association p-values

Thank you for your reply. I'm aware of the permutation function for overall QTL p-values (the

Feb 26

Billy Jiang, Karl Broman3

Feb 19

Haplotype-based QTL vs SNP-based

Thank you! On Tuesday 20 February 2024 at 5:44:27 am UTC+11 Karl Broman wrote: The haplotype-based

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Haplotype-based QTL vs SNP-based

Thank you! On Tuesday 20 February 2024 at 5:44:27 am UTC+11 Karl Broman wrote: The haplotype-based

Feb 19

Fernando Andrade, Karl Broman2

Feb 9

How is permutation done?

See the "Details" section in the help file for scan1perm(): "If kinship is not

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How is permutation done?

See the "Details" section in the help file for scan1perm(): "If kinship is not

Feb 9

Saikat Bandyopadhyay, Karl Broman2

Jan 30

permutation replicates

It depends how you intend to use the permutations. If you're trying to get an estimate of 5%

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permutation replicates

It depends how you intend to use the permutations. If you're trying to get an estimate of 5%

Jan 30

Giovanni Gabelli, … Karl Broman7

12/6/23

QTL analysis in MAGIC populatinon

Great question! I would permute the rows of the genotype data across the BXD strains and then

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QTL analysis in MAGIC populatinon

Great question! I would permute the rows of the genotype data across the BXD strains and then

12/6/23

11/28/23

R/qtl2 version 0.34

A new version of R/qtl2 (version 0.34) has been released on CRAN. Windows and Mac binaries will be

unread,

R/qtl2 version 0.34

A new version of R/qtl2 (version 0.34) has been released on CRAN. Windows and Mac binaries will be

11/28/23

Eduardo Beche, Karl Broman2

11/24/23

How to save a plot in jpge or tiff format

Use a function such as jpeg() or png() in advance of your plotting functions, and then dev.off()

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How to save a plot in jpge or tiff format

Use a function such as jpeg() or png() in advance of your plotting functions, and then dev.off()

11/24/23

Eduardo Beche, Karl Broman2

11/24/23

How find markers name

Use the function find_marker(). karl On Friday, November 24, 2023 at 3:31:03 AM UTC-6 edb...@gmail.

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How find markers name

Use the function find_marker(). karl On Friday, November 24, 2023 at 3:31:03 AM UTC-6 edb...@gmail.

11/24/23

Sabrina Mi, Karl Broman2

11/17/23

negative length vectors are not allowed error

That's wild. Definitely a new one for me. It's hard to see what might be going on without

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negative length vectors are not allowed error

That's wild. Definitely a new one for me. It's hard to see what might be going on without

11/17/23

Christopher Panaretos, … Karl Broman3

11/17/23

R/qtl2 Analysis with CC Mice and "Strain Mean" Phenotypes

Hi, Chris, You may not need to focus on the details in these files. You can load these CC data files

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R/qtl2 Analysis with CC Mice and "Strain Mean" Phenotypes

Hi, Chris, You may not need to focus on the details in these files. You can load these CC data files

11/17/23

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