Entering edit mode
4.1 years ago
francesca3
▴
140
Hi everyone, I'm trying to run csaw on Windows10 x64 system using R 3.6.6 and R 3.6.1 and I'm not able to find some functions, such as filterWindowsGlobal, mergeResults. Besides, when I try to use the filterWindows function putting both the counts and the background, it says that the background and the counts don't have the same library size, but they are produced from the same files.
I loaded all these packages
library(KernSmooth)
library(csaw)
library(limma)
library(readr)
library(edgeR)
library(BiocFileCache)
library(rtracklayer)
library(statmod)
Could be a problem of compatibility? These are my session info
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rsamtools_2.0.3 Biostrings_2.52.0 XVector_0.24.0 readr_1.3.1 KernSmooth_2.23-16
[6] IRkernel_1.1 csaw_1.18.0 edgeR_3.26.8 limma_3.40.6 BiocFileCache_1.8.0
[11] dbplyr_1.4.2 DESeq2_1.24.0 SummarizedExperiment_1.14.1 DelayedArray_0.10.0 BiocParallel_1.18.1
[16] matrixStats_0.56.0 Biobase_2.44.0 GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3
[21] S4Vectors_0.22.1 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 class_7.3-15 IRdisplay_0.7.0 htmlTable_1.13.3 base64enc_0.1-3
[6] rstudioapi_0.11 bit64_0.9-7 AnnotationDbi_1.46.1 prodlim_2019.11.13 lubridate_1.7.4
[11] codetools_0.2-16 splines_3.6.1 geneplotter_1.62.0 knitr_1.28 jsonlite_1.6.1
[16] Formula_1.2-3 pROC_1.16.1 caret_6.0-85 annotate_1.62.0 cluster_2.1.0
[21] png_0.1-7 compiler_3.6.1 httr_1.4.1 backports_1.1.5 assertthat_0.2.1
[26] Matrix_1.2-18 acepack_1.4.1 htmltools_0.4.0 prettyunits_1.1.1 tools_3.6.1
[31] gtable_0.3.0 glue_1.3.2 GenomeInfoDbData_1.2.1 reshape2_1.4.3 dplyr_0.8.5
[36] rappdirs_0.3.1 Rcpp_1.0.3 vctrs_0.2.4 nlme_3.1-140 rtracklayer_1.44.4
[41] iterators_1.0.12 timeDate_3043.102 gower_0.2.1 xfun_0.12 stringr_1.4.0
[46] lifecycle_0.2.0 XML_3.99-0.3 zlibbioc_1.30.0 MASS_7.3-51.5 scales_1.1.0
[51] ipred_0.9-9 hms_0.5.3 RColorBrewer_1.1-2 curl_4.3 memoise_1.1.0
[56] gridExtra_2.3 ggplot2_3.3.0 biomaRt_2.40.5 rpart_4.1-15 latticeExtra_0.6-29
[61] stringi_1.4.6 RSQLite_2.2.0 genefilter_1.66.0 foreach_1.4.8 checkmate_2.0.0
[66] GenomicFeatures_1.36.4 lava_1.6.7 repr_1.1.0 rlang_0.4.5 pkgconfig_2.0.3
[71] bitops_1.0-6 evaluate_0.14 lattice_0.20-38 purrr_0.3.3 GenomicAlignments_1.20.1
[76] recipes_0.1.10 htmlwidgets_1.5.1 bit_1.1-15.2 tidyselect_1.0.0 plyr_1.8.6
[81] magrittr_1.5 R6_2.4.1 generics_0.0.2 Hmisc_4.3-1 pbdZMQ_0.3-3
[86] DBI_1.1.0 pillar_1.4.3 foreign_0.8-71 withr_2.1.2 survival_3.1-11
[91] RCurl_1.98-1.1 nnet_7.3-12 tibble_2.1.3 crayon_1.3.4 uuid_0.1-4
[96] jpeg_0.1-8.1 progress_1.2.2 locfit_1.5-9.1 grid_3.6.1 data.table_1.12.8
[101] blob_1.2.1 ModelMetrics_1.2.2.1 digest_0.6.25 xtable_1.8-4 munsell_0.5.0
Thanks Francesca
As I said before in other threads these open-ended questions are not informative without code. Please add the code that you used. Anecdotal error messages are almost impossible to debug.
The functions you refer to were added in later releases, see https://bioconductor.org/packages/release/bioc/news/csaw/NEWS
Consider upgrading the package.
What are the count windows? The same windows as the background windows? If not then there is your explanation about library sizes.
Hi Francesca,
I was puzzled that some functions were not automatically installed either. But, as ATpoint pointed out, this was because I was viewing the latest manual but then installed a different version of csaw. I was not thinking about version difference as I recently just installed csaw. However, due to my R and bioconductor version, I actually did not install the latest version. Hope this helps!