Question: error: getCTSS from CAGEexp class with removeFirstG=TRUE
0
gravatar for Pengcheng Yang
13 months ago by
China
Pengcheng Yang50 wrote:

Hi, I have successfully installed CAGEr version 1.22.3, and successfully tested the example codes in the CAGEr guides (http://www.bioconductor.org/packages/release/bioc/vignettes/CAGEr/inst/doc/CAGEexp.html). In the CAGEr example, the input is CTSS files. Now, I tested using "bam" format as input files. After constructing the CAGEexp class, I can run run getCTSS with  parameters "correctSystematicG=FALSE,removeFirstG=FALSE". When I set "removeFirstG=TRUE",  the error message said "Error in checkSlotAssignment(object, name, value)". Could this be a bug or my mistake? Thank you!

> i.ce <- CAGEexp(
+     genomeName = "BSgenome.Bterrestris.bcm.bter1",
+     inputFiles = "/path/to/bam/file/file.bam",
+     inputFilesType = "bam",
+     sampleLabels = "test"
+     ) 
> getCTSS(i.ce)

Reading in file: /path/to/bam/file/file.bam...
        -> Filtering out low quality reads...
        -> Removing the first base of the reads if 'G' and not aligned to the genome...
Error in .remove.added.G.CTSS(gr, genome, correctSystematicG = correctSystematicG) :
  correctSystematicG not supported yet for CAGEexp objects
> getCTSS(i.ce,correctSystematicG=FALSE)

Reading in file: /path/to/bam/file/file.bam...
        -> Filtering out low quality reads...
        -> Removing the first base of the reads if 'G' and not aligned to the genome...
Error in checkSlotAssignment(object, name, value) :
  assignment of an object of class "IRanges" is not valid for slot 'ranges' in an object of class "GPos"; is(value, "IPos") is not TRUE
> getCTSS(i.ce,correctSystematicG=FALSE,removeFirstG=FALSE)

Reading in file: /path/to/bam/file/file.bam...
        -> Filtering out low quality reads...

The session information is:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago)

Matrix products: default
BLAS: /histor/kang/yangpc/soft/R/R_soft/lib64/R/lib/libRblas.so
LAPACK: /histor/kang/yangpc/soft/R/R_soft/lib64/R/lib/libRlapack.so

locale:
[1] C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] BSgenome.Bterrestris.bcm.bter1_1.1 BSgenome_1.48.0                  
[3] rtracklayer_1.40.6                 GenomicAlignments_1.16.0         
[5] SummarizedExperiment_1.10.1        DelayedArray_0.6.6               
[7] BiocParallel_1.14.2                matrixStats_0.54.0               
[9] Biobase_2.40.0                     Rsamtools_1.32.3                 
[11] Biostrings_2.48.0                  XVector_0.20.0                   
[13] GenomicRanges_1.32.7               GenomeInfoDb_1.16.0              
[15] IRanges_2.14.12                    S4Vectors_0.18.3                 
[17] BiocGenerics_0.26.0                CAGEr_1.22.3                      

loaded via a namespace (and not attached):
[1] Rcpp_0.12.19               stringdist_0.9.5.1       
[3] lattice_0.20-35            tidyr_0.8.1              
[5] gtools_3.8.1               assertthat_0.2.0         
[7] digest_0.6.17              R6_2.3.0                 
[9] plyr_1.8.4                 ggplot2_3.0.0            
[11] pillar_1.3.0               zlibbioc_1.26.0          
[13] rlang_0.2.2                lazyeval_0.2.1           
[15] data.table_1.11.8          vegan_2.5-2              
[17] Matrix_1.2-14              splines_3.5.0            
[19] RCurl_1.95-4.11            munsell_0.5.0            
[21] compiler_3.5.0             pkgconfig_2.0.2          
[23] mgcv_1.8-23                tidyselect_0.2.4         
[25] tibble_1.4.2               GenomeInfoDbData_1.1.0   
[27] XML_3.98-1.16              reshape_0.8.7            
[29] permute_0.9-4              crayon_1.3.4             
[31] dplyr_0.7.6                MASS_7.3-49              
[33] bitops_1.0-6               grid_3.5.0               
[35] nlme_3.1-137               gtable_0.2.0             
[37] magrittr_1.5               scales_1.0.0             
[39] KernSmooth_2.23-15         stringi_1.2.4            
[41] som_0.3-5.1                MultiAssayExperiment_1.6.0
[43] bindrcpp_0.2.2             tools_3.5.0              
[45] glue_1.3.0                 purrr_0.2.5              
[47] colorspace_1.3-2           cluster_2.0.7-1          
[49] beanplot_1.2               memoise_1.1.0            
[51] VGAM_1.0-6                 bindr_0.1.1  

 

cager • 242 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by Pengcheng Yang50

Hi, I have same errors as you had before. Have you figured them out?  Thanks!

ADD REPLYlink written 10 months ago by guifengwei10

Finally, I have to use

getCTSS(i.ce,correctSystematicG=FALSE,removeFirstG=FALSE)

ADD REPLYlink written 8 months ago by Pengcheng Yang50
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