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aramp10
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@aramp10-15166
Last seen 6.7 years ago
Hi,
I have a custom generated motif database (a single text file of several motifs). I'd like to load this motif database into R for use with motifStack.
I run the following and see this error:
> motifs <- importMatrix(filename, format="meme") Error in switch(alphabet, ACGT = "DNA", ACGU = "RNA", ACDEFGHIKLMNPQRSTVWY = "AA", : EXPR must be a length 1 vector
Is there something wrong with the format of my input file? Is there an example input file with MEME formatted motifs that correctly loads with the importMatrix() function?
If needed, please see my session info below:
> sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.4 (Final) Matrix products: default BLAS: /share/pkg/r/3.4.3/install/lib64/R/lib/libRblas.so LAPACK: /share/pkg/r/3.4.3/install/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel grid stats graphics grDevices utils datasets methods [10] base other attached packages: [1] RColorBrewer_1.1-2 MotifDb_1.20.0 motifStack_1.22.2 Biostrings_2.46.0 [5] XVector_0.18.0 IRanges_2.12.0 S4Vectors_0.16.0 ade4_1.7-10 [9] MotIV_1.34.0 BiocGenerics_0.24.0 grImport_0.9-0 XML_3.98-1.9 loaded via a namespace (and not attached): [1] Rcpp_0.12.14 compiler_3.4.3 GenomeInfoDb_1.14.0 [4] plyr_1.8.4 bitops_1.0-6 tools_3.4.3 [7] zlibbioc_1.24.0 digest_0.6.13 lattice_0.20-35 [10] BSgenome_1.46.0 Matrix_1.2-12 DelayedArray_0.4.1 [13] seqLogo_1.44.0 GenomeInfoDbData_1.0.0 rtracklayer_1.38.2 [16] htmlwidgets_0.9 data.table_1.10.4-3 Biobase_2.38.0 [19] BiocParallel_1.12.0 rGADEM_2.26.0 Rsamtools_1.30.0 [22] scales_0.5.0 matrixStats_0.52.2 htmltools_0.3.6 [25] GenomicAlignments_1.14.1 GenomicRanges_1.30.1 MASS_7.3-48 [28] SummarizedExperiment_1.8.1 splitstackshape_1.4.2 colorspace_1.3-2 [31] RCurl_1.95-4.9 munsell_0.4.3
Thanks,
Andy