当我试图运行路径分析时，如何克服R中MetaboAnalyst的问题？
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我正在使用这段代码 https:/drive.google.comfiled1CXluzyYqNoPqu1DI3HwvDAmRVGMe825mview 为了进行路径分析，使用 MetaboAnalystR.
当我到了这个阶段
mSet<-CalculateOraScore(mSet, "rbc", "hyperg")
我得到这个错误
Loading files from server unsuccessful. Ensure curl is downloaded on your computer
Error in if (is_http) : argument is of length zero
我查看了常见问题和故障排除页面，但无法解决这个问题。我已经在另一台电脑上完成了所有的安装步骤（不幸的是，又是在Windows上，我得到了同样的问题）。
这很可能是Windows上的curl问题。( 我已经在Windows 10上安装了，请看其他问题。当我在Windows 10中使用R ( MetaboAnalyst包)时，我还可以做什么来确保curl工作？).
故障处理建议 https:/github.comxia-labMetaboAnalystRblobmasterRgeneral_data_utils.R。 关于卷曲问题，对我来说也不起作用。
EDIT 2：更大的化合物列表
如果可能的话，我将非常感激，如果有人愿意运行下面的代码，并得到Pathway Impact vs -log(p)的图表，并输出结果，如果需要的话，我可以在图表上注释这些点。代码如下。
library(MetaboAnalystR)
tmp.vec <- c(tmp.vec <- c("Indole-3-carboxylic acid", "4-O-Methylgallic acid", "Hippuric acid", "Pyrocatechol", "Hydroquinone",
"Aspartame", "trans-Ferulic acid", "2,6-Dimethoxyphenol", "2-Methylhippuric acid", "2-(Hydroxymethyl)benzoic acid",
"3-(2-Hydroxyphenyl)propanoic acid", "1-Methyluric acid", "Dehydroisoandrosterone 3-glucuronide", "Ascorbic acid",
"D-Tartaric acid", "Kynurenic acid", "Xanthine", "Vanillic acid", "Glyceraldehyde", "D-Lactic acid", "Pregnanediol",
"7-Methylguanine", "Gluconic acid", "4-Aminophenol", "Caffeic acid", "Enterolactone", "Adipic acid",
"1H-Indole-3-carboxaldehyde", "4-Hydroxybenzoic acid", "Creatinine", "2-Aminobenzoic acid", "Uric acid")
mSet<-InitDataObjects("conc", "pathora", FALSE)
mSet<-Setup.MapData(mSet, tmp.vec);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet);
##4-O-Methylgallic acid and 2-Methylhippuric acid need correct kegg ID format
mSet$dataSet$map.table[2,5] <- "C05616"
mSet$dataSet$map.table[9,5] <- "C01586"
mSet<-SetKEGG.PathLib(mSet, "hsa", "current")
mSet<-SetMetabolomeFilter(mSet, F)
mSet<-CalculateOraScore(mSet, "rbc", "hyperg")
mSet<-PlotPathSummary(mSet, "path_view_0_", "png", 72, width=NA)
答案
在花了至少30分钟安装CRAN和Bioconductor的依赖包后，我得以让代码工作。
如果要我猜测你的问题，你可能还没有安装所有的依赖包。
请按照以下说明进行安装 此处:
#install.packages("pacman")
library(pacman)
pacman::p_load(Rserve, ellipse, scatterplot3d, Cairo, randomForest,
caTools, e1071, som, impute, pcaMethods, RJSONIO, ROCR,
globaltest, GlobalAncova, Rgraphviz, preprocessCore, genefilter,
pheatmap, SSPA, sva, Rcpp, pROC, data.table, limma, car, fitdistrplus,
lars, Hmisc, magrittr, methods, xtable, pls, caret, lattice, igraph,
gplots, KEGGgraph, reshape, RColorBrewer, tibble, siggenes, plotly,
xcms, CAMERA, fgsea, MSnbase)
不管出于什么原因，我也不得不手动安装以下软件包。
BiocManager::install("edgeR")
install.packages("crmn")
devtools::install_github("xia-lab/MetaboAnalystR")
我对你的数据进行了分析。请看下面的输出。
library(MetaboAnalystR)
tmp.vec <- c("Indole-3-carboxylic acid", "4-O-Methylgallic acid", "Hippuric acid", "Pyrocatechol", "Hydroquinone",
"Aspartame", "trans-Ferulic acid", "2,6-Dimethoxyphenol", "2-Methylhippuric acid", "2-(Hydroxymethyl)benzoic acid",
"3-(2-Hydroxyphenyl)propanoic acid", "1-Methyluric acid", "Dehydroisoandrosterone 3-glucuronide", "Ascorbic acid",
"D-Tartaric acid", "Kynurenic acid", "Xanthine", "Vanillic acid", "Glyceraldehyde", "D-Lactic acid", "Pregnanediol",
"7-Methylguanine", "Gluconic acid", "4-Aminophenol", "Caffeic acid", "Enterolactone", "Adipic acid",
"1H-Indole-3-carboxaldehyde", "4-Hydroxybenzoic acid", "Creatinine", "2-Aminobenzoic acid", "Uric acid")
mSet<-InitDataObjects("conc", "pathora", FALSE)
mSet<-Setup.MapData(mSet, tmp.vec)
mSet$dataSet$map.table
Query Match HMDB PubChem KEGG SMILES Comment
[1,] "Indole-3-carboxylic acid" "Indole-3-carboxylic acid" "HMDB0003320" "69867" "C19837" "C1=CC=C2C(=C1)C(=CN2)C(=O)O" "1"
[2,] "4-O-Methylgallic acid" "4-O-Methylgallic acid" "HMDB0013198" "78016" NA "COC1=C(C=C(C=C1O)C(=O)O)O" "1"
[3,] "Hippuric acid" "Hippuric acid" "HMDB0000714" "464" "C01586" "C1=CC=C(C=C1)C(=O)NCC(=O)O" "1"
[4,] "Pyrocatechol" "Pyrocatechol" "HMDB0000957" "3390" "C15571" "C1=CC=C(C(=C1)O)O" "1"
[5,] "Hydroquinone" "Hydroquinone" "HMDB0002434" "785" "C00530" "C1=CC(=CC=C1O)O" "1"
[6,] "Aspartame" "Aspartame" "HMDB0001894" "134601" "C11045" "COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@H](CC(=O)O)N" "1"
[7,] "trans-Ferulic acid" "trans-Ferulic acid" "HMDB0000954" "445858" "C01494" "COC1=C(C=CC(=C1)/C=C/C(=O)O)O" "1"
[8,] "2,6-Dimethoxyphenol" "2,6-Dimethoxyphenol" "HMDB0034158" "7041" "C10787" "COC1=C(C(=CC=C1)OC)O" "1"
[9,] "2-Methylhippuric acid" "2-Methylhippuric acid" "HMDB0011723" "91637" "\t C01586" "CC1=CC=CC=C1C(=O)NCC(=O)O" "1"
[10,] "2-(Hydroxymethyl)benzoic acid" "2-(Hydroxymethyl)benzoic acid" "HMDB0032594" "11920" "C10804" "C1=CC=C(C(=C1)CO)C(=O)O" "1"
[11,] "3-(2-Hydroxyphenyl)propanoic acid" "3-(2-Hydroxyphenyl)propanoic acid" "HMDB0033752" "873" "C01198" "C1=CC=C(C(=C1)CCC(=O)O)O" "1"
[12,] "1-Methyluric acid" "1-Methyluric acid" "HMDB0003099" "69726" "C16359" "CN1C(=O)C2=C(NC(=O)N2)NC1=O" "1"
[13,] "Dehydroisoandrosterone 3-glucuronide" "Dehydroisoandrosterone 3-glucuronide" "HMDB0010327" "53480448" "C03033" "CC12CCC3C(C1CCC2=O)CC=C4C3(CCC(C4)O[C@H]5[C@@H]([C@H]([C@@H](C(O5)C(=O)O)O)O)O)C" "1"
[14,] "Ascorbic acid" "Ascorbic acid" "HMDB0000044" "54670067" "C01041" "C([C@@H]([C@@H]1C(=C(C(=O)O1)O)O)O)O" "1"
[15,] "D-Tartaric acid" "D-Tartaric acid" "HMDB0029878" "439655" "C02107" "[C@H]([C@@H](C(=O)O)O)(C(=O)O)O" "1"
[16,] "Kynurenic acid" "Kynurenic acid" "HMDB0000715" "3845" "C01717" "C1=CC=C2C(=C1)C(=O)C=C(N2)C(=O)O" "1"
[17,] "Xanthine" "Xanthine" "HMDB0000292" "1188" "C00385" "C1=NC2=C(N1)C(=O)NC(=O)N2" "1"
[18,] "Vanillic acid" "Vanillic acid" "HMDB0000484" "8468" "C06672" "COC1=C(C=CC(=C1)C(=O)O)O" "1"
[19,] "Glyceraldehyde" "Glyceraldehyde" "HMDB0001051" "751" "C02154" "C(C(C=O)O)O" "1"
[20,] "D-Lactic acid" "D-Lactic acid" "HMDB0001311" "61503" "C00256" "C[C@H](C(=O)O)O" "1"
[21,] "Pregnanediol" "Pregnanediol" "HMDB0004025" "3032822" "C05484" "CC[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4[C@@]3(CCC(C4)(O)O)C)C" "1"
[22,] "7-Methylguanine" "7-Methylguanine" "HMDB0000897" "11361" "C02242" "CN1C=NC2=C1C(=O)N=C(N2)N" "1"
[23,] "Gluconic acid" "Gluconic acid" "HMDB0000625" "10690" "C00257" "C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O" "1"
[24,] "4-Aminophenol" "4-Aminophenol" "HMDB0001169" "403" "C02372" "C1=CC(=CC=C1N)O" "1"
[25,] "Caffeic acid" "Caffeic acid" "HMDB0001964" "1549111" "C01481" "C1=CC(=C(C=C1/C=C\\C(=O)O)O)O" "1"
[26,] "Enterolactone" "Enterolactone" "HMDB0006101" "123917" "C18165" "C1C(C(C(=O)O1)CC2=CC(=CC=C2)O)CC3=CC(=CC=C3)O" "1"
[27,] "Adipic acid" "Adipic acid" "HMDB0000448" "196" "C06104" "C(CCC(=O)O)CC(=O)O" "1"
[28,] "1H-Indole-3-carboxaldehyde" "1H-Indole-3-carboxaldehyde" "HMDB0029737" "10256" "C08493" "C1=CC=C2C(=C1)C(=CN2)C=O" "1以上是关于当我试图运行路径分析时，如何克服R中MetaboAnalyst的问题？的主要内容，如果未能解决你的问题，请参考以下文章
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