Closed:KEGGREST -- gene list
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Haiying.Kong ▴ 110
@haiyingkong-9254
Last seen 6.8 years ago
Germany

library(KEGGREST)

> names(keggGet("map07049")[[1]])
[1] "ENTRY"       "NAME"        "PATHWAY_MAP" "COMPOUND"    "REFERENCE"

I need to get gene list (hugo-symbol) in each pathway. How can I get this from KEGGREST?

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE 13.1 (Bottle) (x86_64)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] KEGGREST_1.14.1

loaded via a namespace (and not attached):
 [1] zlibbioc_1.20.0     httr_1.3.1          R6_2.2.2
 [4] IRanges_2.8.2       XVector_0.14.1      parallel_3.3.3
 [7] tools_3.3.3         curl_3.1            Biostrings_2.42.1
[10] S4Vectors_0.12.2    BiocGenerics_0.20.0 stats4_3.3.3
[13] png_0.1-7

 

bioconductor • 66 views
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