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anc.informatics
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@ancinformatics-17655
Last seen 6.2 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