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Question: no import.bam function in CAGEr version 1.22.3
1
gravatar for Pengcheng Yang
6 days ago by
China
Pengcheng Yang50 wrote:

Hi, I found there is no import.bam function in the latest version (1.22.3) of CAGEr. However, the import.bam function has been documented in the reference manual of CAGEr (http://www.bioconductor.org/packages/release/bioc/manuals/CAGEr/man/CAGEr.pdf)

 

 

> library(CAGEr)
> 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 6.3 (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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] CAGEr_1.22.3

loaded via a namespace (and not attached):
 [1] stringdist_0.9.5.1          SummarizedExperiment_1.10.1
 [3] gtools_3.8.1                splines_3.5.0              
 [5] lattice_0.20-35             colorspace_1.3-2           
 [7] htmltools_0.3.6             stats4_3.5.0               
 [9] mgcv_1.8-23                 beanplot_1.2               
[11] rtracklayer_1.40.6          XML_3.98-1.16              
[13] rlang_0.2.2                 later_0.7.5                
[15] pillar_1.3.0                BiocParallel_1.14.2        
[17] BiocGenerics_0.26.0         matrixStats_0.54.0         
[19] GenomeInfoDbData_1.1.0      plyr_1.8.4                 
[21] zlibbioc_1.26.0             Biostrings_2.48.0          
[23] munsell_0.5.0               gtable_0.2.0               
[25] VGAM_1.0-6                  memoise_1.1.0              
[27] Biobase_2.40.0              permute_0.9-4              
[29] IRanges_2.14.12             httpuv_1.4.5               
[31] MultiAssayExperiment_1.0.1  GenomeInfoDb_1.16.0        
[33] parallel_3.5.0              Rcpp_0.12.19               
[35] KernSmooth_2.23-15          xtable_1.8-3               
[37] promises_1.0.1              scales_1.0.0               
[39] som_0.3-5.1                 BSgenome_1.48.0            
[41] DelayedArray_0.6.6          vegan_2.5-2                
[43] S4Vectors_0.18.3            XVector_0.20.0             
[45] mime_0.6                    Rsamtools_1.32.3           
[47] ggplot2_3.0.0               digest_0.6.17              
[49] stringi_1.2.4               shiny_1.1.0                
[51] GenomicRanges_1.32.7        grid_3.5.0                 
[53] tools_3.5.0                 bitops_1.0-6               
[55] magrittr_1.5                RCurl_1.95-4.11            
[57] lazyeval_0.2.1              tibble_1.4.2               
[59] cluster_2.0.7-1             crayon_1.3.4               
[61] MASS_7.3-49                 Matrix_1.2-14              
[63] data.table_1.11.8           shinydashboard_0.7.0       
[65] reshape_0.8.7               R6_2.3.0                   
[67] nlme_3.1-137                GenomicAlignments_1.16.0   
[69] compiler_3.5.0             
> import
importIntoEnv     importPublicData  
> import.bam()
Error in import.bam() : could not find function "import.bam"
> 

Update

It turned out that this function can be got from the source file: 

git clone https://git.bioconductor.org/packages/CAGEr

source("CAGEr/R/ImportMethods.R")

 

ADD COMMENTlink modified 5 days ago • written 6 days ago by Pengcheng Yang50
1

Hi, this function (and a bunch of others) are "private" in the sense that they are not exported and not expected to be directly useful to most users.  Sorry that the documentation is not clear about this.  You can also call it by prefixing its name with the package name (CAGEr:::import.bam).  In any case, if you would like to load BAM files in a CAGEr object, you have to construct a CAGEr object as explained in the vignette, with the inputFiles parameter pointing to the files and the inputFilesType parameter set to "bam".

ADD REPLYlink written 5 days ago by Charles Plessy90

Hi, Charles Plessy, thank you for your reply. I have successfully run the function through CAGEr:::import.bam. However, another problem about `bam2CTSS` has been encountered. Please help me. I have posted the problem in a new thread (https://support.bioconductor.org/p/113813/)

 

ADD REPLYlink written 5 days ago by Pengcheng Yang50
1

Can you mark the questions as answered if your problems were solved ?  This will help me to track the open issues.  Thanks !

ADD REPLYlink written 5 days ago by Charles Plessy90

OK! To mark the answered question. I have added the answer and marked it. Thank you!

ADD REPLYlink written 5 days ago by Pengcheng Yang50
1
gravatar for Pengcheng Yang
5 days ago by
China
Pengcheng Yang50 wrote:

This problem has been solved by Charles Plessy in the comment, and detailed below:

The import.bam function can be accessed by: CAGEr:::import.bam

ADD COMMENTlink written 5 days ago by Pengcheng Yang50
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