Methread error Error in data[, 5] * data[, 6] : non-numeric argument to binary operator
1
0
Entering edit mode
hasche • 0
@37f4c9de
Last seen 2.6 years ago
United States

Hi, I am trying to run methylkit with my bismark output (genome wide cytosine report.txt). I am using the following code-

Code should be placed in three backticks as shown below

include your problematic code here with any corresponding output

file.list=list("CpG_context_3292_oxbs_bismark_bt2_pe.genomewidecoverage.CpG_report.txt", "CpG_context_3293_bs_bismark_bt2_pe.genomewidecoverage.CpG_report.txt") myobj=methRead(file.list, sample.id=list("CpG_context_3292_oxbs_bismark_bt2_pe.genomewidecoverage.CpG_report.txt", "CpG_context_3293_bs_bismark_bt2_pe.genomewidecoverage.CpG_report.txt"), assembly="hg38",treatment=c(1,0))

My error- Received list of locations.Reading file. |--------------------------------------------------| |==================================================| Error in data[, 5] * data[, 6] : non-numeric argument to binary operator

please also include the results of running the following in an R session

sessionInfo( ) R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.4

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] methylKit_1.18.0 remotes_2.4.0 bsseq_1.28.0 SummarizedExperiment_1.22.0 Biobase_2.52.0 MatrixGenerics_1.4.0
[7] matrixStats_0.59.0 GenomicRanges_1.44.0 Biostrings_2.60.0 GenomeInfoDb_1.28.0 XVector_0.32.0 IRanges_2.26.0
[13] S4Vectors_0.30.0 BiocGenerics_0.38.0

loaded via a namespace (and not attached): [1] splines_4.1.0 DelayedMatrixStats_1.14.0 R.utils_2.10.1 gtools_3.9.2 BiocManager_1.30.15 BSgenome_1.60.0
[7] GenomeInfoDbData_1.2.6 Rsamtools_2.8.0 yaml_2.2.1 numDeriv_2016.8-1.1 pillar_1.6.1 lattice_0.20-44
[13] glue_1.4.2 limma_3.48.0 bbmle_1.0.23.1 qvalue_2.24.0 colorspace_2.0-1 Matrix_1.3-4
[19] R.oo_1.24.0 plyr_1.8.6 XML_3.99-0.6 pkgconfig_2.0.3 emdbook_1.3.12 zlibbioc_1.38.0
[25] purrr_0.3.4 mvtnorm_1.1-1 scales_1.1.1 HDF5Array_1.20.0 BiocParallel_1.26.0 tibble_3.1.2
[31] generics_0.1.0 ggplot2_3.3.3 ellipsis_0.3.2 mclust_5.4.7 magrittr_2.0.1 crayon_1.4.1
[37] R.methodsS3_1.8.1 fansi_0.5.0 MASS_7.3-54 tools_4.1.0 data.table_1.14.0 BiocIO_1.2.0
[43] lifecycle_1.0.0 stringr_1.4.0 Rhdf5lib_1.14.0 munsell_0.5.0 locfit_1.5-9.4 DelayedArray_0.18.0
[49] compiler_4.1.0 fastseg_1.38.0 rlang_0.4.11 rhdf5_2.36.0 grid_4.1.0 RCurl_1.98-1.3
[55] rhdf5filters_1.4.0 rjson_0.2.20 bitops_1.0-7 restfulr_0.0.13 gtable_0.3.0 curl_4.3.1
[61] reshape2_1.4.4 R6_2.5.0 GenomicAlignments_1.28.0 dplyr_1.0.6 rtracklayer_1.52.0 bdsmatrix_1.3-4
[67] utf8_1.2.1 permute_0.9-5 stringi_1.6.2 Rcpp_1.0.6 vctrs_0.3.8 tidyselect_1.1.1
[73] sparseMatrixStats_1.4.0 coda_0.19-4
```

methylkit • 1.4k views
ADD COMMENT
0
Entering edit mode
alex.gos90 ▴ 10
@alexgos90-13597
Last seen 3 months ago
Germany

Hi @drhasnachetia,

You need to change the pipeline argument of the methRead() function to indicate you are providing a Bismark cytosine report (bismarkCytosineReport), otherwise methRead assumes you are providing the default amp format.

Best, Alex

ADD COMMENT

Login before adding your answer.

Traffic: 991 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6