When subsetting a qPCRset, the current implementation fails to transfer the featureData. Here is a fix:
diff --git a/R/qPCRset.R b/R/qPCRset.R index d400ea5..cecef29 100644 --- a/R/qPCRset.R +++ b/R/qPCRset.R @@ -73,6 +73,7 @@ function(x, i, j, drop=FALSE) { featureCategory=featureCategory(x)[i, j, drop=FALSE], flag=flag(x)[i, j, drop=FALSE]) phenoData(out) <- phenoData(x)[j,,drop=FALSE] + featureData(out) <- featureData(x)[i,,drop=FALSE] featureNames(out) <- featureNames(x)[i] out })
Hi Henrik,
I wanted to include your function modification but, in the corresponding folder in my R library (mylib/HTqPCR/R), I do not find any R file corresponding to the qPCRset function. I've looked around in other folders but I don't find it...
Where do you include this code? Does it belong to another package called by HTqPCR? I'm a bit confused.
Thanks a lot!
Sarah
sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux release 6.9 (Carbon)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BiocInstaller_1.28.0 HTqPCR_1.32.0 limma_3.34.9
[4] RColorBrewer_1.1-2 Biobase_2.38.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] gtools_3.5.0 bitops_1.0-6 affy_1.56.0
[4] stats4_3.4.3 KernSmooth_2.23-15 gplots_3.0.1
[7] zlibbioc_1.24.0 gdata_2.18.0 affyio_1.48.0
[10] preprocessCore_1.40.0 tools_3.4.3 compiler_3.4.3
[13] caTools_1.17.1 tcltk_3.4.3
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