Question: Pathview input error: non-numeric variable in data frame
0
gravatar for anc.informatics
13 months ago by
anc.informatics0 wrote:

I tried to map some Human genes to KEGG pathways using pathview library. However, an error occurred.  Can someone point out the error?

library("pathview")
    geneList = read.table("list.txt", sep="\t", header=TRUE)
    hsa04110 <- pathview(gene.data  = geneList,
                     pathway.id = "hsa04110",
                     species    = "hsa",
                     limit      = list(gene=max(abs(geneList)), cpd=1))

 

'list.txt' file contains human gene ids and values. For example,

id    fc
hsa04110    1
hsa04114    2
hsa04218    3

output of sessioninfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] pathview_1.20.0      org.Hs.eg.db_3.5.0   AnnotationDbi_1.40.0
[4] IRanges_2.12.0       S4Vectors_0.16.0     Biobase_2.38.0      
[7] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] graph_1.56.0      Rcpp_0.12.15      KEGGgraph_1.38.0  XVector_0.18.0   
 [5] zlibbioc_1.24.0   bit_1.1-12        R6_2.2.2          rlang_0.2.0      
 [9] blob_1.1.0        httr_1.3.1        tools_3.4.3       grid_3.4.3       
[13] png_0.1-7         DBI_0.8           bit64_0.9-7       digest_0.6.15    
[17] tibble_1.4.2      Rgraphviz_2.22.0  KEGGREST_1.18.1   memoise_1.1.0    
[21] RSQLite_2.0       compiler_3.4.3    pillar_1.2.1      Biostrings_2.46.0
[25] XML_3.98-1.3      pkgconfig_2.0.1

 

 

 

 

 

pathways pathview kegg package • 272 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by anc.informatics0
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