I came across a problem when trying to run pathview() to map gene expression data to KEGG.
1. I run this code:
pathview(gene.data = gene_matrix,
pathway.id = "04070",
species = "mouse")
The structure of the input object gene_matrix is shown as followed:
head(gene_matrix)
497097 27395 21399 240690 319263 71096
0.6876964 0.4142183 1.4401079 -1.0009338 0.4017501 0.7701214
I got this error:
Error in UseMethod("select_") :
**no applicable method for 'select_' applied to an object of class "c('OrgDb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')"**
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", :
replacement has 29 rows, data has 49
2. The environment where I run the program was rstudio-server, which was installed on Cent OS 7 and R version was 3.4.4.
Detailed information is listed below:
> R.Version()
$platform
[1] "x86_64-redhat-linux-gnu"
$arch
[1] "x86_64"
$os
[1] "linux-gnu"
$system
[1] "x86_64, linux-gnu"
$status
[1] ""
$major
[1] "3"
$minor
[1] "4.4"
$year
[1] "2018"
$month
[1] "03"
$day
[1] "15"
$`svn rev`
[1] "74408"
$language
[1] "R"
$version.string
[1] "R version 3.4.4 (2018-03-15)"
$nickname
[1] "Someone to Lean On"
3. What puzzled me was that there seemed to be no problem with the pathview package, because I tested it with the demo data and the pathview() function worked well.
I run this code:
library(pathview)
data(gse16873.d)
pv.out <- pathview(gene.data = gse16873.d[, 1],
pathway.id = "04110",
species = "hsa",
out.suffix = "gse16873")
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/**/R/**/**
Info: Writing image file hsa04110.gse16873.png
In addition, both the codes I run above (in green) worked well on RStudio built on Win 10.
The result of the first code is shown below:
pathview(gene.data = gene_matrix,
pathway.id = "04070",
species = "mouse")
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory E:/**/R/**
Info: Writing image file mmu04070.pathview.png
There were 50 or more warnings (use warnings() to see the first 50)
The version of RStudio is 1.1.423 and the version of R is 3.4.2.
I really appreciate any help you offer. Thanks.
