Pathview input error: non-numeric variable in data frame
0
0
Entering edit mode
@ancinformatics-17655
Last seen 5.5 years ago

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

 

 

 

 

 

pathview kegg pathways package • 950 views
ADD COMMENT

Login before adding your answer.

Traffic: 497 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6