Entering edit mode
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")
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 loadBAMfiles in aCAGErobject, you have to construct aCAGErobject as explained in the vignette, with theinputFilesparameter pointing to the files and theinputFilesTypeparameter set to"bam".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/).
Can you mark the questions as answered if your problems were solved ? This will help me to track the open issues. Thanks !
OK! To mark the answered question. I have added the answer and marked it. Thank you!