Methread error Error in data[, 5] * data[, 6] : non-numeric argument to binary operator
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hasche • 0
@37f4c9de
Last seen 5 months 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 • 421 views
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Entering edit mode
alex.gos90 ▴ 10
@alexgos90-13597
Last seen 4 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

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