Hello,
I am a new user of DEXSeq and I would need some help concerning an error message I get and I cannot solve.
My sample table looks like this:
> phenodata samplename condition bu1 bulge_1 bulge bu2 bulge_2 bulge bu3 bulge_3 bulge le1 lef1_1 lef1 le4 lef1_4 lef1 le5 lef1_5 lef1 le6 lef1_6 lef1
I am trying to create an ExonCountSet object but I get an error message:
> library(DEXSeq) > ec = HTSeqCounts(countfiles=c("bulge_1.txt","bulge_2.txt","bulge_3.txt","lef_1.txt","lef_4.txt","lef_5.txt","lef_6.txt"), design=phenodata) Error: could not find function "HTSeqCounts"
Even if the DEXSeq package seems to be loaded as seen in the session Info:
R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.4 (El Capitan) locale: [1] C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.20.1 DEXSeq_1.16.10 DESeq2_1.10.1 [4] RcppArmadillo_0.6.700.3.0 Rcpp_0.12.4 SummarizedExperiment_1.0.2 [7] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8 [10] S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1 [13] BiocParallel_1.4.3 loaded via a namespace (and not attached): [1] genefilter_1.52.1 statmod_1.4.24 locfit_1.5-9.1 splines_3.2.3 [5] lattice_0.20-33 colorspace_1.2-6 survival_2.39-2 XML_3.98-1.4 [9] foreign_0.8-66 DBI_0.3.1 RColorBrewer_1.1-2 lambda.r_1.1.7 [13] plyr_1.8.3 stringr_1.0.0 zlibbioc_1.16.0 Biostrings_2.38.4 [17] munsell_0.4.3 gtable_0.2.0 futile.logger_1.4.1 hwriter_1.3.2 [21] latticeExtra_0.6-28 geneplotter_1.48.0 biomaRt_2.26.1 AnnotationDbi_1.32.3 [25] acepack_1.3-3.3 xtable_1.8-2 scales_0.4.0 Hmisc_3.17-3 [29] annotate_1.48.0 XVector_0.10.0 Rsamtools_1.22.0 gridExtra_2.2.1 [33] ggplot2_2.1.0 stringi_1.0-1 grid_3.2.3 tools_3.2.3 [37] bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.8 RSQLite_1.0.0 [41] Formula_1.2-1 cluster_2.0.4 futile.options_1.0.0 Matrix_1.2-5 [45] rsconnect_0.4.2.1 rpart_4.1-10 nnet_7.3-12
Does anyone know why I have this error message?
Thanks in advance for your help,
Sakura
I realised that I had an error, I was supposed to type "read.HTSeqCounts()" instead of just "HTSeqCounts()", but id did not solve my problem, I still get:
Error: could not find function "read.HTSeqCounts"
I am trying to follow the pipeline from this source, and it seems that this function is in the package...
https://books.google.co.jp/books?id=f4tqBAAAQBAJ&pg=PA184&lpg=PA184&dq=Reading+all+the+sample-specific+count+tables+is+done+by+the+function+read.HTSeqCounts()+from+the+package+DEXSeq&source=bl&ots=7lMhp7fVjQ&sig=r6dEc-4slTppnDK8ODVD4RMzJHg&hl=fr&sa=X&ved=0ahUKEwii3vuu46HMAhWGtpQKHaoRDtYQ6AEIHjAA#v=onepage&q=Reading%20all%20the%20sample-specific%20count%20tables%20is%20done%20by%20the%20function%20read.HTSeqCounts()%20from%20the%20package%20DEXSeq&f=false
I think the function has been renamed as
DEXSeqDataSetFromHTSeq()
, and the chapter that you are using is (already, unfortunately) out-of-date (I couldn't find via online search the version of DEXSeq used in the chapter -- nosessionInfo()
). Some archaeology shows that read.HTSeqCount was 'deprecated' on 2014-03-21, in version 1.9.7 of the package, so more than two years ago; the current version of the package is 1.16.10. The message accompanying the change isso there may be additional differences between the text of the book that you are reading and the package. The good news is that there is an extensive current vignette (also
browseVignettes(package="DEXSeq")
) in the package itself.And this is written in that vignette about HTSeq
The initial steps of a DEXSeq analysis, described in the following two sections, is typically done outside R, by using two provided Python scripts
Thank you all for your answers. I changed the method and I am now following this pipeline as you suggested. However, I also have some problems.
When I call the DEXSeqDataSetFromHTSeq, I obtain the following error:
Here is what countFiles and sampleTable look like:
I guess this is correct. However, when looking at the count files, I have the impression that the .txt look weird. Here is the first one (sample: basal_1) as an example. This is all that is contained in the file:
_ambiguous 0
_ambiguous_readpair_position 0
_empty 9651846
_lowaqual 846199
_notaligned 421258
I created this file with this command (and successfully installed pysam before):
Is this output normal with dexseq_count.py? If not, does anyone know what could be the problem? I tried with different options, but as my data are not paired-end and strand specific, I should use is like this.