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1 ###############################################################################
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2 # title: MethylGSA
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3 # author: Xiaowei
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4 # time: Mar.31 2021
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5 ###############################################################################
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6
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7 spec <- matrix(c("data_file", "D",1, "character", "txt file",
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8 "test_method","M",1,"character", "Test method",
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9 "array_type","T",1,"character","Array type, 450K, EPCI",
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10 "group","G",1,"character","group: all, body, promoter1, promoter2",
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11 "GS_list","L",1,"character","Gene Set tested: Gene Ontology, KEGG, Reactome",
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12 "minsize","I",1,"integer", "Minimum gene set size",
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13 "maxsize","A",1,"integer", "Maximum gene set size",
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14 "result", "R", 1, "character", "result table"
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15 ), byrow = TRUE, ncol = 5)
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16
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17 opt <- getopt::getopt(spec)
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18
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19
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20 # #===========================================================================
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21 # #输入的参数
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22 # #===========================================================================
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23 # # txt文件
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24 # opt$data_file
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25 # opt$test_method
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26 # opt$array_type
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27 # opt$group
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28 # opt$GS_list
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29 # opt$minsize
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30 # opt$maxsize
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31
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32
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33 temp = read.table(opt$data_file)
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34 cpg.pval1 = temp[,2]
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35 names(cpg.pval1) = temp[,1]
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36 inputmethod = opt$test_method
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37
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38 #================================================================
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39 #run codes
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40 #================================================================
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41 suppressPackageStartupMessages(library(methylGSA))
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42
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43
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44 if(opt$array_type=="450K"){
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45 suppressMessages(library(IlluminaHumanMethylation450kanno.ilmn12.hg19))
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46 }else{
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47 suppressMessages(library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19))
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48 }
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49
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50 if(inputmethod == "methylglm"){
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51 res <- methylglm(cpg.pval = cpg.pval1, array.type = opt$array_type,
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52 group = opt$group, GS.list=NULL,
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53 GS.idtype = "SYMBOL", GS.type = opt$GS_list,
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54 minsize = opt$minsize, maxsize = opt$maxsize)
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55
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56 }
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57
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58 if(inputmethod == "RRA_ORA"){
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59 res <- methylRRA(cpg.pval = cpg.pval1, array.type = opt$array_type,
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60 group = opt$group, method = "ORA",
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61 GS.list=NULL, GS.idtype = "SYMBOL", GS.type = opt$GS_list,
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62 minsize = opt$minsize, maxsize = opt$maxsize)
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63 }
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64
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65 if(inputmethod == "RRA_GSEA"){
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66 res <- methylRRA(cpg.pval = cpg.pval1, array.type = opt$array_type,
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67 group = opt$group, method = "GSEA",
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68 GS.list=NULL, GS.idtype = "SYMBOL", GS.type = opt$GS_list,
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69 minsize = opt$minsize, maxsize = opt$maxsize)
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70 }
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71
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72 if(inputmethod == "gometh"){
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73 res <- methylgometh(cpg.pval = cpg.pval1, sig.cut = 0.001, array.type = opt$array_type,
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74 GS.list=NULL, GS.idtype = "SYMBOL", GS.type = opt$GS_list,
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75 minsize = opt$minsize, maxsize = opt$maxsize)
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76 }
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77
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78 #===============================================================================
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79 write.csv(res, file = opt$result)
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