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Question: Trying to load several MEME formatted motifs for use in motifStack
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gravatar for aramp10
6 months ago by
aramp100
aramp100 wrote:

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

ADD COMMENTlink written 6 months ago by aramp100
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