R/qtl2 version 0.22

[Karl Broman]

We've released a new version of R/qtl2. Install the update with

    update.packages(ask=FALSE, repos="https://rqtl.org/qtl2cran")

Or install from scratch with

    install.packages("qtl2", repos="https://rqtl.org/qtl2cran")

The changes are shown below. R/qtl2fst and R/qtl2convert have also been updated.

karl

---

Major changes

• Added some functions for diagnostics: recode_snps(),
  calc_raw_het(), calc_raw_geno_freq(), calc_raw_maf(), and
  calc_raw_founder_maf().

• Added argument blup to fit1(), for getting BLUPs for a single
  fixed QTL position. At present, just gives estimates and
  coefficients by calling scan1blup() with a single position.

• pull_genoprobpos() can now take either a marker name (as before) or
  a set of map, chromosome, and position (from which it uses
  find_marker() to get the marker name).

• Added plot function for the results of compare_geno(). (Plots
  histogram of upper triangle.)

• Added functions n_founders() and founders() for getting the
  number of founders and the founder strain names for a cross2 object.

• scan1() now takes an optional hsq argument, so that the residual
  heritability may be specified rather than estimated.

Minor changes

• write_control_file() now allows cross info codes with a cross info
  file (previously only allowed with a covariate). read_cross2()
  gives a warning if there are cross info conversion codes but more
  than one cross info column.

• Small fix in read_cross2() to allow multiple cross info covariates.

• Added a check that the founder genotypes have the same strain IDs on
  each chromosome.

• convert2cross2() now includes alleles component even if it
  wasn't present as an attribute.

• Added function sdp2char() for converting numeric SDP codes to
  character strings like "ABC|DEFGH".

• Updated mouse gene database with 2019-08-12 data from
  MGI.

• get_common_ids() strips off names from output, just in case.

• Added internal functions rqtl1_crosstype() and rqtl1_chrtype().

Bug fixes

• Fixed typo in help for scan1() and related functions.

• genoprob_to_snpprob() was giving an error if you gave a cross2
  object in place of a snpinfo table and it had monomorphic markers.

• Fixed problem with weights in scan1() and related functions when
  their derived from table(). Make sure they're a plain numeric
  vector, not an array.

• Fixed check_cross2(): the check for invalid genotypes wasn't
  happening.

• Better error message for the case that there are no markers in
  common between map and genotypes.

• extract_dim_from_header(), used by read_cross2() and read_csv(),
  now just looks for the number part in the rest of the line.

• maxlod() now handles missing values (forcing na.rm=TRUE). If all
  values are missing it gives a warning and returns -Inf.
  [Fixes Issue #134.]

• In max_scan1(), treat the case that the input has no column names.
  [Fixes Issue #133.]

• max_scan1() was giving a messed up error message if lodcolumn
  was out of range. [Fixes Issue #132.]

• Revised the script inst/scripts/create_ccvariants.R to capture all
  of the consequences and genes for each SNP (rather than just the
  first), and fixing a bug that prevented capture of indels from
  chromosomes 6-X. Consequently, revised the example SQLite database
  extdata/cc_variants_small.sqlite and associated tests.

[Soren]

Dear Carl, 

after I updated the qtl2 package, I can't seem to load it any more. My R is 3.6.3 and R studio is 1.3.959. I get the following error when I load the package:

> install.packages("qtl2", repos="https://rqtl.org/qtl2cran")

Installing package into ‘/Users/dqz393/Library/R/3.6/library’

(as ‘lib’ is unspecified)

trying URL 'https://rqtl.org/qtl2cran/bin/macosx/el-capitan/contrib/3.6/qtl2_0.22.tgz'

Content type 'application/octet-stream' length 2605709 bytes (2.5 MB)

==================================================

downloaded 2.5 MB

The downloaded binary packages are in

/var/folders/rx/xb_n10_n6vn5dby079nyzghd3qnd_m/T//RtmpDdUXIZ/downloaded_packages

> library(qtl2)

Error: package or namespace load failed for ‘qtl2’ in dyn.load(file, DLLpath = DLLpath, ...):

 unable to load shared object '/Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so':

  dlopen(/Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so, 6): Symbol not found: ____chkstk_darwin

  Referenced from: /Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so

  Expected in: /usr/lib/libSystem.B.dylib

 in /Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so

It seem like it cannot find the file.

I've tried to uninstall both the package and R.

Thanks in advance!
Søren

[Karl Broman]

What version of Mac OS X are you using?

Can you show me the output of R.version?

karl

[Soren]

Hi again, thanks for your quick reply!

I'm running on MacOS Sierra, version 10.12.6.

I get the following when I try to install it straight in to R console (R 3.6.3 GUI 1.70 El Capitan build (7735)):

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"

Copyright (C) 2020 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin15.6.0 (64-bit)

[R.app GUI 1.70 (7735) x86_64-apple-darwin15.6.0]

[Workspace restored from /Users/dqz393/.RData]

[History restored from /Users/dqz393/.Rapp.history]

> install.packages("qtl2", repos="https://rqtl.org/qtl2cran")

Installing package into ‘/Users/dqz393/Library/R/3.6/library’

(as ‘lib’ is unspecified)

trying URL 'https://rqtl.org/qtl2cran/bin/macosx/el-capitan/contrib/3.6/qtl2_0.22.tgz'

Content type 'application/octet-stream' length 2605709 bytes (2.5 MB)

==================================================

downloaded 2.5 MB

The downloaded binary packages are in

/var/folders/rx/xb_n10_n6vn5dby079nyzghd3qnd_m/T//Rtmp98QJ01/downloaded_packages

> library(qtl2)

Error: package or namespace load failed for ‘qtl2’ in dyn.load(file, DLLpath = DLLpath, ...):

 unable to load shared object '/Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so':

  dlopen(/Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so, 6): Symbol not found: ____chkstk_darwin

  Referenced from: /Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so

  Expected in: /usr/lib/libSystem.B.dylib

 in /Users/dqz393/Library/R/3.6/library/qtl2/libs/qtl2.so

Søren

On Friday, May 22, 2020 at 4:12:45 PM UTC+10, Karl Broman wrote:

[Karl Broman]

You could try installing it from source

   install.packages(“qtl2”, repos=“https://rqtl.org/qtl2cran”, type=“source”)

You’d need to install Xcode. At the command line:

   xcode-select --install

karl

[Karl Broman]

I think the trouble is that I compiled the package on MacOS Catalina, 10.15, and it's apparently not backward-compatible. Looks like CRAN is using 10.13 to build packages (https://mac.r-project.org).

I'll see if I can build useable versions. But it seems like it's time for me to put qtl2 onto CRAN.

I'm sorry for these problems,

karl

On Tuesday, May 26, 2020 at 7:00:07 AM UTC-5, Soren wrote:

[Soren]

Hi again, installing it straight from the source did the trick! Thanks a lot for your help!
kind regards,

Søren

On Friday, May 22, 2020 at 4:12:45 PM UTC+10, Karl Broman wrote:

[Ramesh S. Bhat]

Dear Dr. Karl,

May I know the functions to get BLUPs for a single fixed QTL position?

I think scan1blup() and fit1() with an argument blup are no longer active.

Kind regards,

 

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[Karl Broman]

You can use fit1() to get BLUPs for a fixed position.

karl

[Ramesh S. Bhat]

But, I get the following result

 ?fit1
No documentation for ‘fit1’ in specified packages and libraries:
you could try ‘??fit1’

To view this discussion on the web visit https://groups.google.com/d/msgid/rqtl2-disc/2b80a5b7-88ad-4e57-a14b-62a2e700fa3cn%40googlegroups.com.

[Ramesh S. Bhat]

I shall try again.

On Wed, May 29, 2024 at 4:26 PM Karl Broman <kbr...@gmail.com> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/rqtl2-disc/2b80a5b7-88ad-4e57-a14b-62a2e700fa3cn%40googlegroups.com.

[Karl Broman]

You maybe need to load the package.

    library(qtl2)

karl

[Ramesh S. Bhat]

Yes, you are right.
Is there any function in the package "qtl" to get the blup?

To view this discussion on the web visit https://groups.google.com/d/msgid/rqtl2-disc/8b26df36-b9de-44f4-8974-e83cd7de310dn%40googlegroups.com.

[Dan Gatti]

I don’t believe that there is. I would use qtl2.

 

Dan

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[Karl Broman]

No.

karl