GSEA-R误差R的Mac OSX埃尔卡皮坦

Question

不知道有多少人还使用R脚本GSEA，但是当我尝试加载脚本及其功能：

GSEA.program.location <- ("file location of GSEA.1.0.R") 
source(GSEA.program.location, verbose=T, max.deparse.length=9999) 

我得到这个错误

'envir' chosen:<environment: R_GlobalEnv> 
encoding = "native.enc" chosen 
Error: '\%' is an unrecognized escape in character string starting ""Tag \%" 

我相信我必须删除退格，但我已经通过GSEA.1.0.R和“源代码”函数源代码进行了搜索，而且我找不到这个'\％'。我做错了什么？

Session info: 
R version 3.2.2 (2015-08-14) 
Platform: x86_64-apple-darwin13.4.0 (64-bit) 
Running under: OS X 10.11.1 (El Capitan) 

locale: 
[1] C/C/C/C/C/en_GB.UTF-8 

attached base packages: 
[1] stats graphics grDevices utils datasets methods base  

other attached packages: 
[1] biomaRt_2.26.0 WGCNA_1.48 RSQLite_1.0.0 DBI_0.3.1 fastcluster_1.1.16 dynamicTreeCut_1.62 

loaded via a namespace (and not attached): 
[1] reshape2_1.4.1  splines_3.2.2   lattice_0.20-33  colorspace_1.2-6  htmltools_0.2.6  
[6] stats4_3.2.2   yaml_2.1.13   survival_2.38-3  XML_3.98-1.3   foreign_0.8-66  
[11] BiocGenerics_0.16.1 RColorBrewer_1.1-2 matrixStats_0.15.0 foreach_1.4.3   plyr_1.8.3   
[16] stringr_1.0.0   munsell_0.4.2   gtable_0.1.2   codetools_0.2-14  latticeExtra_0.6-26 
[21] Biobase_2.30.0  IRanges_2.4.1   doParallel_1.0.10  parallel_3.2.2  AnnotationDbi_1.32.0 
[26] preprocessCore_1.32.0 GSEABase_1.32.0  proto_0.3-10   Rcpp_0.12.1   acepack_1.3-3.3  
[31] xtable_1.8-0   scales_0.3.0   S4Vectors_0.8.1  Hmisc_3.17-0   graph_1.48.0   
[36] annotate_1.48.0  gridExtra_2.0.0  impute_1.44.0   ggplot2_1.0.1   digest_0.6.8   
[41] stringi_1.0-1   grid_3.2.2   tools_3.2.2   bitops_1.0-6   magrittr_1.5   
[46] RCurl_1.95-4.7  Formula_1.2-1   cluster_2.0.3   GO.db_3.2.2   MASS_7.3-45   
[51] rmarkdown_0.8.1  iterators_1.0.8  rpart_4.1-10   nnet_7.3-11 

Answer 1

为什么不尝试GSEApy，它很容易使用并支持很多库。在这里看到：https://github.com/BioNinja/gseapy

安装：

conda install -c bioconda gseapy 

或使用PIP：

pip install gseapy 

Answer 2

当你具有R版本2.5和更高版本会出现这些警告。要修复，请删除这些字符前面的单个反斜杠，因为在R版本2.5和更高版本中不需要转义它们。