IgGeneUsage: computational tool for the analysis of differential gene usage (DGU) in B- and T-cell receptor repertoires.
For more information see vignettes in folder vignette/.
Comparison of gene usage in immune repertoires under different biological conditions
License: MIT License
Intentional?
Hi,
I tried to test your igGeneUsage on my Windows pc, but get error below, please help me!!!
Thank you
Joan
M <- DGU(usage.data = IGHV_HCV, # input data
mcmc.warmup = 250, # how many MCMC warm-ups per chain (default: 500)
mcmc.steps = 1000, # how many MCMC steps per chain (default: 1,500)
mcmc.chains = 2, # how many MCMC chain to run (default: 4)
mcmc.cores = 1, # how many PC cores to use? (e.g. parallel chains)
hdi.level = 0.95, # highest density interval level (de fault: 0.95)
adapt.delta = 0.95, # MCMC target acceptance rate (default: 0.95)
max.treedepth = 10) # tree depth evaluated at each step (default: 12)
Compiling model ...
make cmd is
make -f "C:/PROGRA1/R/R-421.1/etc/x64/Makeconf" -f "C:/PROGRA1/R/R-421.1/share/make/winshlib.mk" CXX='$(CXX14)
make would use
if test "zfile6e843f2f6e5b.o" != "z"; then
if test -e "file6e843f2f6e5b-win.def"; then
echo g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll file6e843f2f6e5b-win.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll file6e843f2f6e5b-win.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
else
echo EXPORTS > tmp.def;
nm file6e843f2f6e5b.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def;
echo g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll tmp.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
g++ -shared -s -static-libgcc -o file6e843f2f6e5b.dll tmp.def file6e843f2f6e5b.o -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64" -L"C:/rtools42/x86_64-w64-mingw32.static.posix/lib" -L"C:/PROGRA1/R/R-421.1/bin/x64" -lR ;
rm -f tmp.def;
fi
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to
tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file6e843f2f6e5b.o:file6e843f2f6e5b.cpp:(.text$_ZN3tbb10interface
In addition: Warning message:
In checkUsageData(usage.data = usage.data) :
no replicates provided for at least one of the conditions.
Error in sink(type = "output") : invalid connection
Paired vs. replicated setup check details
While LOOIC analysis does not "recommend" that with the given datasets, this might be useful.
What to pay attention to:
Allow user to modify priors (big re-design will be needed)
Hi -- the chunks in the vignette are all eval=F
? This prevents the Bioconductor build system from
realistically checking the package. I tried running the vignette (changing eval=F to eval=TRUE,
and using IgGeneUsage:::DGU because DGU function is not exported) and after two chains finish
we have:
Computing summaries ...
Posterior extraction ...
Computing probability of DGU ...
Computing posterior predictions ...
Error: $ operator is invalid for atomic vectors
In addition: Warning messages:
1: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
2: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess
Enter a frame number, or 0 to exit
1: source("IgUsageCaseStudies.R", echo = TRUE)
2: withVisible(eval(ei, envir))
3: eval(ei, envir)
4: eval(ei, envir)
5: IgUsageCaseStudies.R#64: IgGeneUsage:::DGU(usage.data = IGHV_HCV, mcmc.warm
6: getPpcRepertoire(glm = glm, usage.data = usage.data, hdi.level = hdi.level)
> sessionInfo()
R version 4.2.0 RC (2022-04-15 r82209)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /home/stvjc/R-4-2-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-4-2-dist/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] reshape2_1.4.4 rstan_2.21.5
[3] ggrepel_0.9.1 gridExtra_2.3
[5] ggforce_0.3.3 ggplot2_3.3.6
[7] IgGeneUsage_1.11.1 StanHeaders_2.21.0-7
[9] SummarizedExperiment_1.26.1 Biobase_2.56.0
[11] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[13] IRanges_2.30.0 S4Vectors_0.34.0
[15] BiocGenerics_0.42.0 MatrixGenerics_1.8.0
[17] matrixStats_0.62.0 Rcpp_1.0.8.3
[19] knitr_1.39 rmarkdown_2.14
loaded via a namespace (and not attached):
[1] lattice_0.20-45 prettyunits_1.1.1 ps_1.7.0
[4] assertthat_0.2.1 digest_0.6.29 utf8_1.2.2
[7] plyr_1.8.7 R6_2.5.1 evaluate_0.15
[10] highr_0.9 pillar_1.7.0 zlibbioc_1.42.0
[13] rlang_1.0.2 callr_3.7.0 Matrix_1.4-1
[16] startup_0.18.0 labeling_0.4.2 stringr_1.4.0
[19] loo_2.5.1 RCurl_1.98-1.6 polyclip_1.10-0
[22] munsell_0.5.0 DelayedArray_0.22.0 compiler_4.2.0
[25] xfun_0.31 pkgconfig_2.0.3 pkgbuild_1.3.1
[28] htmltools_0.5.2 tidyselect_1.1.2 tibble_3.1.7
[31] GenomeInfoDbData_1.2.8 codetools_0.2-18 fansi_1.0.3
[34] crayon_1.5.1 dplyr_1.0.9 withr_2.5.0
[37] MASS_7.3-57 bitops_1.0-7 grid_4.2.0
[40] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[43] magrittr_2.0.3 scales_1.2.0 RcppParallel_5.1.5
[46] cli_3.3.0 stringi_1.7.6 farver_2.1.0
[49] XVector_0.36.0 ellipsis_0.3.2 generics_0.1.2
[52] vctrs_0.4.1 tools_4.2.0 glue_1.6.2
[55] tweenr_1.0.2 purrr_0.3.4 parallel_4.2.0
[58] processx_3.6.0 fastmap_1.1.0 inline_0.3.19
[61] colorspace_2.0-3
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