Question: Pathview input error: non-numeric variable in data frame
0
gravatar for anc.informatics
3 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

 

 

 

 

 

package kegg pathways pathview • 124 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by anc.informatics0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 186 users visited in the last hour