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10
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1 clusterSize=2
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2 class(clusterSize)
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3 type(clusterSize)
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4 require("minfi", quietly = TRUE)
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5 ??getGenomicRatioSetFromGEO
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6 getGenomicRatioSetFromGEO
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7 getwd()
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8 GEODataTable <- getGEO(GSE51547)
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9 require("BiocGenerics", quietly = TRUE)
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10 require("data.table", quietly = TRUE)
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11 require("GEOquery", quietly = TRUE)
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12 require("rtracklayer", quietly = TRUE)
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13 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
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14 GEODataTable <- getGEO(GSE51547)
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15 GEODataTable <- getGEO("GSE51547")
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16 IlmnIDTable <- Table(GEODataTable)
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17 MetaData <- data.frame(Meta(GEODataTable))
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18 IlmnIDTable <- Table(GEODataTable)
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19 GEODataTable
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20 GSE<-"GSE51547"
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21 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
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22 annotation = .default.450k.annotation, what = c("Beta", "M"),
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23 mergeManifest = FALSE, i = 1)
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24 {
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25 what <- match.arg(what)
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26 if (is.null(GSE) && is.null(path))
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27 stop("Either GSE or path must be supplied.")
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28 if (!is.null(GSE))
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29 gset <- GEOquery::getGEO(GSE)
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30 else gset <- GEOquery::getGEO(filename = file.path(path,
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31 list.files(path, pattern = ".soft")))
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32 if (length(gset) == 0)
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33 stop("Empty list retrieved from GEO.")
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34 if (length(gset) > 1) {
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35 warning("More than one ExpressionSet found:\n", names(gset),
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36 "\nUsing entry ", i)
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37 gset <- gset[[i]]
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38 }
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39 else gset <- gset[[1]]
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40 platform <- annotation(gset)
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41 if (platform != "GPL13534")
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42 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
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43 platform))
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44 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
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45 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
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46 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
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47 ann <- .getAnnotationString(c(array = array, annotation = annotation))
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48 if (!require(ann, character.only = TRUE))
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49 stop(sprintf("cannot load annotation package %s", ann))
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50 object <- get(ann)
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51 gr <- getLocations(object, mergeManifest = mergeManifest,
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52 orderByLocation = TRUE)
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53 locusNames <- names(gr)
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54 sampleNames(gset) <- gset$title
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55 common <- intersect(locusNames, fData(gset)$Name)
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56 if (length(common) == 0)
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57 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
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58 ind1 <- match(common, fData(gset)$Name)
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59 ind2 <- match(common, locusNames)
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60 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
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61 if (what == "Beta") {
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62 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
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63 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
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64 annotation = c(array = array, annotation = annotation),
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65 preprocessMethod = preprocessing)
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66 }
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67 else {
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68 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
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69 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
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70 pData = pData(gset), annotation = c(array = array,
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71 annotation = annotation), preprocessMethod = preprocessing)
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72 }
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73 return(out)
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74 }
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75 <environment: namespace:minfi>
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76 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
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77 annotation = .default.450k.annotation, what = c("Beta", "M"),
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78 mergeManifest = FALSE, i = 1)
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79 {
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80 what <- match.arg(what)
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81 if (is.null(GSE) && is.null(path))
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82 stop("Either GSE or path must be supplied.")
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83 if (!is.null(GSE))
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84 gset <- GEOquery::getGEO(GSE)
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85 else gset <- GEOquery::getGEO(filename = file.path(path,
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86 list.files(path, pattern = ".soft")))
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87 if (length(gset) == 0)
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88 stop("Empty list retrieved from GEO.")
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89 if (length(gset) > 1) {
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90 warning("More than one ExpressionSet found:\n", names(gset),
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91 "\nUsing entry ", i)
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92 gset <- gset[[i]]
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93 }
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94 else gset <- gset[[1]]
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95 platform <- annotation(gset)
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96 if (platform != "GPL13534")
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97 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
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98 platform))
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99 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
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100 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
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101 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
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102 ann <- .getAnnotationString(c(array = array, annotation = annotation))
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103 if (!require(ann, character.only = TRUE))
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104 stop(sprintf("cannot load annotation package %s", ann))
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105 object <- get(ann)
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106 gr <- getLocations(object, mergeManifest = mergeManifest,
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107 orderByLocation = TRUE)
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108 locusNames <- names(gr)
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109 sampleNames(gset) <- gset$title
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110 common <- intersect(locusNames, fData(gset)$Name)
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111 if (length(common) == 0)
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112 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
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113 ind1 <- match(common, fData(gset)$Name)
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114 ind2 <- match(common, locusNames)
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115 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
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116 if (what == "Beta") {
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117 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
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118 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
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119 annotation = c(array = array, annotation = annotation),
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120 preprocessMethod = preprocessing)
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121 }
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122 else {
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123 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
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124 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
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125 pData = pData(gset), annotation = c(array = array,
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126 annotation = annotation), preprocessMethod = preprocessing)
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127 }
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128 return(out)
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129 }
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130 GSE<-"GSE51547"
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131 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
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132 annotation = .default.450k.annotation, what = c("Beta", "M"),
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133 mergeManifest = FALSE, i = 1)
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134 {
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135 what <- match.arg(what)
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136 if (is.null(GSE) && is.null(path))
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137 stop("Either GSE or path must be supplied.")
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138 if (!is.null(GSE))
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139 gset <- GEOquery::getGEO(GSE)
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140 else gset <- GEOquery::getGEO(filename = file.path(path,
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141 list.files(path, pattern = ".soft")))
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142 if (length(gset) == 0)
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143 stop("Empty list retrieved from GEO.")
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144 if (length(gset) > 1) {
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145 warning("More than one ExpressionSet found:\n", names(gset),
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146 "\nUsing entry ", i)
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147 gset <- gset[[i]]
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148 }
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149 else gset <- gset[[1]]
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150 platform <- annotation(gset)
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151 if (platform != "GPL13534")
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152 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
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153 platform))
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154 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
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155 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
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156 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
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157 ann <- .getAnnotationString(c(array = array, annotation = annotation))
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158 if (!require(ann, character.only = TRUE))
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159 stop(sprintf("cannot load annotation package %s", ann))
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160 object <- get(ann)
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161 gr <- getLocations(object, mergeManifest = mergeManifest,
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162 orderByLocation = TRUE)
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163 locusNames <- names(gr)
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164 sampleNames(gset) <- gset$title
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165 common <- intersect(locusNames, fData(gset)$Name)
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166 if (length(common) == 0)
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167 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
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168 ind1 <- match(common, fData(gset)$Name)
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169 ind2 <- match(common, locusNames)
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170 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
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171 if (what == "Beta") {
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172 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
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173 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
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174 annotation = c(array = array, annotation = annotation),
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175 preprocessMethod = preprocessing)
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176 }
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177 else {
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178 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
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179 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
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180 pData = pData(gset), annotation = c(array = array,
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181 annotation = annotation), preprocessMethod = preprocessing)
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182 }
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183 return(out)
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184 }
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185 out
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186 GSE<-"GSE51547"
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187 gset <- getGEO(GSE)
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188 ann <- .getAnnotationString(c(array = array, annotation = annotation))
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189 platform <- annotation(gset)
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190 hm450.hg19 <- getPlatform()
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191 IlmnInfo <-
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192 data.table(
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193 IlmnID = names(hm450.hg19),
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194 CHR = as.data.frame(hm450.hg19@seqnames)$value,
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195 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
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196 )
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197 IlmnIDTable <- Table(gset)
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198 ??getGenomicRatioSetFromGEO()
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199 getGenomicRatioSetFromGEO()
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200 getGenomicRatioSetFromGEO
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