binarise_files(indir = "path") maybe this code was an error code ?
sixone11 opened this issue · 6 comments
I try the GSE dataset as you used, but everytime it reports error , I checked the source code and the source code may be confusing at the function. But i was not sure if it was my fault.
Hoping you can check it again,thank you very much
Hi,
Could you please be more specific and post the error you get here as a reply? Just to mention that I have updated the package (both Melissa and BPRMeth which Melissa depends) so you need to install them from Github, as I mention in this reply: #3 (comment)
Also, in the command binarise_files(indir = "path"), the "path" should be set to the path directory you have stored the coverage files.
Thank you for you replying!
I checked it again, and the "path" is the directory I have stored the cov.gz files. It still has some errors.
Sample GSM1370569_Ser15.cov.txt already processed, skipping...
Sample GSM1370572_Ser18.cov.txt already processed, skipping...
Sample GSM1370573_Ser19.cov.txt already processed, skipping...
Sample GSM1370574_Ser20.cov.txt already processed, skipping...
Processing binarised...
gzip: stdin: Is a directory
Error in setnames(x, value) :
Can't assign 5 names to a 0 column data.table
In addition: Warning message:
In data.table::fread(cmd = sprintf("zcat < %s", filename), verbose = FALSE, :
File '/tmp/RtmpnxFbWe/file5bfb7ff85a39' has size 0. Returning a NULL data.table.
Hi,
From the error message it seems to me that you are using an earlier version of Melissa and (possibly) BPRMeth.
Could you first try and install the latest development version from Github:
# Install BPRMeth
devtools::install_github("andreaskapou/BPRMeth")
# Install Melissa
devtools::install_github("andreaskapou/Melissa")and after that you should delete the binarised folder that was created and try and rerun the binarise_files function.
If you still get errors, could you please send me again the error message together with the version of packages you are using, so it's easier for me to help.
Best,
Andreas
Thank you so much for your kind reply!
After I update the package 'BPRMeth', the command:binarise_files(indir = "path") can work pefectly.
But when I added the annotation file,it reminded me there was something wrong.
The format of my annotation file is like
chr1 28735 29810 * CGI
chr1 135124 135563 * CGI
chr1 327790 328229 * CGI
chr1 437151 438164 * CGI
chr1 449273 450544 * CGI
and my command is like below:
library(Melissa)
binarise_files(indir = "gz/CT")
system('gzip gz/CT/binarised/*')
anno<-read_anno(file="cpgIslandExt.BRPMeth.txt")
melissa_data <- create_melissa_data_obj(met_dir = "gz/CT/binarised",
anno_file=anno, cov = 3)
and the error message is :
Error in data.table::fread(input = file, sep = delimiter, stringsAsFactors = FALSE, :
input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or, the input data itself containing at least one \n or \r
and the information about the platform and packages were as follow:
R version 4.0.0 (2020-04-24)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)
Matrix products: default
BLAS/LAPACK: /data/sixone/software/anaconda2/R/4.0.0/lib/libopenblasp-r0.3.9.so
locale:
[1] C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Melissa_1.5.3 BPRMeth_1.14.0 GenomicRanges_1.40.0
[4] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[7] BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 pillar_1.4.4 compiler_4.0.0
[4] BiocManager_1.30.10 XVector_0.28.0 iterators_1.0.12
[7] bitops_1.0-6 tools_4.0.0 zlibbioc_1.34.0
[10] mclust_5.4.6 digest_0.6.25 lattice_0.20-41
[13] evaluate_0.14 lifecycle_0.2.0 tibble_3.0.1
[16] gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.6
[19] foreach_1.5.0 Matrix_1.2-18 yaml_2.2.1
[22] mvtnorm_1.1-0 SparseM_1.78 xfun_0.14
[25] coda_0.19-3 GenomeInfoDbData_1.2.3 knitr_1.28
[28] MatrixModels_0.4-1 vctrs_0.3.0 grid_4.0.0
[31] cowplot_1.0.0 glue_1.4.1 data.table_1.12.8
[34] R6_2.4.1 rmarkdown_2.2 ggplot2_3.3.1
[37] magrittr_1.5 codetools_0.2-16 mcmc_0.9-7
[40] MASS_7.3-51.6 htmltools_0.4.0 scales_1.1.1
[43] ellipsis_0.3.1 matrixcalc_1.0-3 assertthat_0.2.1
[46] BiocStyle_2.16.0 colorspace_1.4-1 quantreg_5.55
[49] MCMCpack_1.4-8 RCurl_1.98-1.2 munsell_0.5.0
[52] truncnorm_1.0-8 crayon_1.3.4
Sorry to bother you again, and hoping for your reply soon!
Have you tried passing the annotation file path to the create_melissa_data_obj method instead of calling read_anno separately?
And maybe use an absolute path at first to make sure that it's not some relative path issue.
Closing issue.