DEMIMessages: A 'list' of DEMI messages
In demi: Differential Expression from Multiple Indicators
Description
Usage
Format
Author(s)
Description
This list contains all the messages shown to the user when running DEMI analysis. It
is used internally in DEMI analysis.
Usage
1
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List of 33
$ demiequal :List of 3
..$ main : chr "# Clustering probes into 'equal' cluster based on Wilcoxon rank sum test if the groups are bigger than 2\n"
..$ custom.approach : chr "\tUsing an optimized implementation to perform Wilcoxon rank sum test\n"
..$ standard.approach: chr "\tUsing the native implementation of the Wilcoxon rank sum test (function 'wilcox.test')\n"
$ demi.wilcox.test.fast :List of 3
..$ main : chr "# Clustering probes into 'higher' and 'lower' clusters based on Wilcoxon rank sum test\n"
..$ custom.approach : chr "\tUsing an optimized implementation to perform Wilcoxon rank sum test\n"
..$ standard.approach: chr "\tUsing the native implementation of the Wilcoxon rank sum test (function 'wilcox.test')\n"
$ demi.wilcox.test :List of 3
..$ main : chr "# Clustering probes into 'higher' and 'lower' clusters based on Wilcoxon rank sum test\n"
..$ exact.false: chr "\tUsing wilcox with parameter 'exact = FALSE' since sample sizes are sufficiently large.\n"
..$ exact.true : chr "\tUsing wilcox with parameter 'exact = TRUE'.\n"
$ demiExperiment_t.test :List of 1
..$ main: chr "# Clustering probes into 'higher' and 'lower' clusters based on t-test (function 't.test')\n"
$ demi.comp.test :List of 1
..$ main: chr "# Clustering probes into 'higher' and 'lower' clusters\n"
$ takestime :function (no.of.probes)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 41 15 41 131 29 145 41 41
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ probesdone :function (no.of.probes)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 42 16 42 99 30 113 42 42
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ sectionsizeMissing :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 49 24 49 118 38 132 49 49
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ positiveIntegerOrZero :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 50 27 50 117 41 131 50 50
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ sectionsizeUse :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 52 20 52 107 34 121 52 52
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ parameterOfClassMissing :function (parameter, cls)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 53 29 53 130 43 144 53 53
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ paramAndParamNotEqualLength:function (param1, param2)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 54 33 54 142 47 156 54 54
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ wrongDefinition :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 55 21 58 94 35 150 55 58
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ savingWhatTo :function (what, to)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 59 18 59 82 32 96 59 59
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ customTargets :List of 11
..$ whatMissingFrom :function (what, from)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 64 23 64 132 51 160 64 64
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ pmsizeMissing : chr "# Note: column 'pmsize' is unspecified in the 'blat' object. We will therefore assume that all probe matches to the target are "| __truncated__
..$ startMissing : chr "# Note: column 'start' is unspecified in the 'blat' object.\n"
..$ strandMissing : chr "# Note: column 'strand' is unspecified in the 'blat' object. We will therefore assume that all probe matches were on the major "| __truncated__
..$ probesNotPresent :function (notpresent)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 68 24 68 198 52 226 68 68
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ geneMissing : chr "# Note: column 'geneID' is missing from the 'anno' object. Will duplicate 'targetID' as 'geneID' \n"
..$ annoMissing : chr "# Note: 'anno' has not been specified. Creating custom annotation\n"
..$ ignoreStrand :function (strand)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 71 20 71 111 48 139 71 71
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ pmsizeSmallerRemove: chr "# Note: Removing probes with perfect match size less than indicated in the DEMIExperiment object\n"
..$ determineMatches : chr "# Determining the number of hits on each target for every probe\n"
..$ error : chr "You can't add custom region alignments's and annotation info to the exon analysis. You can only add them to 'transcript' and 'g"| __truncated__
$ DEMIPathway :List of 2
..$ main : chr "# Performing pathway analysis of differentially expressed genes\n"
..$ cantrun: chr "DEMIPathway can only be run if the analysis type in DEMIExperimebt object is a \"gene\" or \"transcript\"\n"
$ DEMIClust :List of 4
..$ noCELFilesWithGroupname:function (groupName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 84 31 85 136 59 192 84 85
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ usingBuiltIn : chr "# Note: Clustering with demi built-in functions\n"
..$ usingCreaterOrLower : chr "# Note: A heuristic-based method will be used to assess probe-level differential expression as one of the group sizes is <= 2.\"| __truncated__
..$ usingUserProvided : chr "# Note: Clustering with user-provided function\n"
$ DEMIDiff :List of 12
..$ zeroTargetsFound : chr "0 specified targets were found in the experiment"
..$ calcDiffExp : chr "# Calculating differential expression "
..$ betweenGroups :function (groupA, groupB)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 96 21 96 178 49 206 96 96
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ onUserDefined : chr "on user-defined clusters\n"
..$ analyzingClusterNative:function (clusterName, groupA, groupB)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 98 30 98 246 58 274 98 98
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ analyzingClusterCustom:function (clusterName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 99 30 99 135 58 163 99 99
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ calcHyperGeo : chr "\t\tCalculating hypergeometric distribution p-values ... "
..$ annotatingResults : chr "\t\tAnnotating results ..."
..$ multipleCorrectionBH : chr "\t\tAdjusting p-values for multiple testing by the FDR method (Benjamini & Hochberg, 1995) ... "
..$ multipleCorrectionBY : chr "\t\tAdjusting p-values for multiple testing by the FDR method under dependence (Benjamini & Yekutieli, 2001) ... "
..$ multipleCorrectionBONF: chr "\t\tAdjusting p-values for multiple testing by the Bonferroni method ... "
..$ diffExpDone : chr "# Calculating differential expression ... DONE\n"
$ DEMIExperiment :List of 31
..$ invalidWhatChooseFrom :function (what, chooseFrom)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 112 29 112 188 57 216 112 112
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ notFolder :function (parameter)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 113 17 113 91 45 119 113 113
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ folderEmpty :function (parameter)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 114 19 114 130 47 158 114 114
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ notACELFile :function (file, parameter)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 115 19 115 135 47 163 115 115
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ maxprobesError : chr "The parameter 'maxprobes' has to be a positive integer or set as 'median', 'max' or not defined at all which by default set's i"| __truncated__
..$ probesExcluded :function (excludedProbes)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 117 22 117 195 50 223 117 117
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ noTargetsFound : chr "No targets were found"
..$ noProbesMeasuring : chr "No probes measuring the specified targets matched the experiment criteria"
..$ attachErrorResultsExists:function (variable)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 120 32 120 288 60 316 120 120
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ attachErrorDiffDEMIExp : chr "Can't add results of class 'DEMIDiff' to this experiment of class 'DEMIExperiment' because they represent different 'DEMIExperi"| __truncated__
..$ loadingCEL : chr "# Loading CEL files and creating expression matrix\n"
..$ includedCELFiles :function (celfiles)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 123 24 123 115 52 143 123 123
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ usingMicroarrayPlatform :function (platform)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 124 31 124 120 59 148 124 124
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ libraryNotInstalled :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 125 27 125 114 55 142 125 125
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ searchingInternetRepo :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 126 29 126 142 57 170 126 126
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ packageNotFoundFromRepo :function (packageName, package_url)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 127 31 127 143 59 171 127 127
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ installingPackage :function (packageName, repository)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 128 25 128 142 53 170 128 128
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ checkYourInternet : chr "The current operation could not access the internet. Please check your internet connectction"
..$ loadingAnnoSuccess :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 130 26 130 133 54 161 130 130
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ loadingAnnoFail :function (annoTableName, packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 131 23 131 179 51 207 131 131
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ sectionsizeNotAvail :function (sectionsizes)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 132 27 132 169 55 197 132 132
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ cantLoadWhatTable :function (whatTable)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 133 25 133 116 53 144 133 133
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ loadingBlatSuccess :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 134 26 134 132 54 160 134 134
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ blatDoesNotExists :function (blat, platform, packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 135 25 135 192 53 220 135 135
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ pmsizeNotAvail :function (pmsizes)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 136 22 136 182 50 210 136 136
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ ignoreStrandMatches :function (strand)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 137 27 137 112 55 140 137 137
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ loadingCytoband : chr "# Loading cytoband information\n"
..$ loadingPathway : chr "# Loading pathway information\n"
..$ check4probeError :function (difference)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 140 24 142 124 52 173 140 142
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ check4targetError :function (notfound)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 143 25 143 181 53 209 143 143
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ zeroTargetsFound : chr "0 specified targets were found in the experiment"
$ DEMIResults :List of 2
..$ resultsContain : chr "the results list can only contain objects of class 'DEMIResult'"
..$ resultsUndefined: chr "no results have been defined"
$ diffexp :List of 2
..$ matchesCluster: chr "\t\tCalculating matches for probes in cluster ... "
..$ matchesAll : chr "\t\tCalculating matches over all probes ... "
$ normalization :List of 3
..$ main : chr "# Normalizing expression values "
..$ normrrank : chr " - using 'relative rank' as the normalization method\n"
..$ normquantile: chr "- using 'quantile normalization' as the normalization method\n"
$ parameterMissing :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 171 22 171 93 36 107 171 171
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ parameterNotOfClass :function (parameter, cls)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 172 25 172 116 39 130 172 172
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ isNotError :function (parameter, what)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 173 16 173 93 30 107 173 173
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ hasToBeNumericBetween :function (parameter, start, end)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 174 27 174 142 41 156 174 174
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ tooManyParameters :function (parameter, len)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 175 23 175 111 37 125 175 175
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ positiveInteger :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 176 21 176 106 35 120 176 176
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ positiveIntegerUpTo :function (parameter, to)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 177 25 177 124 39 138 177 177
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ hasToBeFunction :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 178 21 178 98 35 112 178 178
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ notEmptyString :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 179 20 179 101 34 115 179 179
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ done :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 180 10 180 32 24 46 180 180
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ demiStart :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 184 15 195 111 29 139 184 195
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
Author(s)
Sten Ilmjarv, Hendrik Luuk
demi documentation built on May 2, 2019, 11:11 a.m.
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Description Usage Format Author(s)
Description
This list contains all the messages shown to the user when running DEMI analysis. It
is used internally in DEMI analysis.
Usage
1 |
Format
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 | List of 33
$ demiequal :List of 3
..$ main : chr "# Clustering probes into 'equal' cluster based on Wilcoxon rank sum test if the groups are bigger than 2\n"
..$ custom.approach : chr "\tUsing an optimized implementation to perform Wilcoxon rank sum test\n"
..$ standard.approach: chr "\tUsing the native implementation of the Wilcoxon rank sum test (function 'wilcox.test')\n"
$ demi.wilcox.test.fast :List of 3
..$ main : chr "# Clustering probes into 'higher' and 'lower' clusters based on Wilcoxon rank sum test\n"
..$ custom.approach : chr "\tUsing an optimized implementation to perform Wilcoxon rank sum test\n"
..$ standard.approach: chr "\tUsing the native implementation of the Wilcoxon rank sum test (function 'wilcox.test')\n"
$ demi.wilcox.test :List of 3
..$ main : chr "# Clustering probes into 'higher' and 'lower' clusters based on Wilcoxon rank sum test\n"
..$ exact.false: chr "\tUsing wilcox with parameter 'exact = FALSE' since sample sizes are sufficiently large.\n"
..$ exact.true : chr "\tUsing wilcox with parameter 'exact = TRUE'.\n"
$ demiExperiment_t.test :List of 1
..$ main: chr "# Clustering probes into 'higher' and 'lower' clusters based on t-test (function 't.test')\n"
$ demi.comp.test :List of 1
..$ main: chr "# Clustering probes into 'higher' and 'lower' clusters\n"
$ takestime :function (no.of.probes)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 41 15 41 131 29 145 41 41
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ probesdone :function (no.of.probes)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 42 16 42 99 30 113 42 42
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ sectionsizeMissing :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 49 24 49 118 38 132 49 49
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ positiveIntegerOrZero :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 50 27 50 117 41 131 50 50
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ sectionsizeUse :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 52 20 52 107 34 121 52 52
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ parameterOfClassMissing :function (parameter, cls)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 53 29 53 130 43 144 53 53
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ paramAndParamNotEqualLength:function (param1, param2)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 54 33 54 142 47 156 54 54
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ wrongDefinition :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 55 21 58 94 35 150 55 58
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ savingWhatTo :function (what, to)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 59 18 59 82 32 96 59 59
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ customTargets :List of 11
..$ whatMissingFrom :function (what, from)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 64 23 64 132 51 160 64 64
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ pmsizeMissing : chr "# Note: column 'pmsize' is unspecified in the 'blat' object. We will therefore assume that all probe matches to the target are "| __truncated__
..$ startMissing : chr "# Note: column 'start' is unspecified in the 'blat' object.\n"
..$ strandMissing : chr "# Note: column 'strand' is unspecified in the 'blat' object. We will therefore assume that all probe matches were on the major "| __truncated__
..$ probesNotPresent :function (notpresent)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 68 24 68 198 52 226 68 68
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ geneMissing : chr "# Note: column 'geneID' is missing from the 'anno' object. Will duplicate 'targetID' as 'geneID' \n"
..$ annoMissing : chr "# Note: 'anno' has not been specified. Creating custom annotation\n"
..$ ignoreStrand :function (strand)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 71 20 71 111 48 139 71 71
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ pmsizeSmallerRemove: chr "# Note: Removing probes with perfect match size less than indicated in the DEMIExperiment object\n"
..$ determineMatches : chr "# Determining the number of hits on each target for every probe\n"
..$ error : chr "You can't add custom region alignments's and annotation info to the exon analysis. You can only add them to 'transcript' and 'g"| __truncated__
$ DEMIPathway :List of 2
..$ main : chr "# Performing pathway analysis of differentially expressed genes\n"
..$ cantrun: chr "DEMIPathway can only be run if the analysis type in DEMIExperimebt object is a \"gene\" or \"transcript\"\n"
$ DEMIClust :List of 4
..$ noCELFilesWithGroupname:function (groupName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 84 31 85 136 59 192 84 85
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ usingBuiltIn : chr "# Note: Clustering with demi built-in functions\n"
..$ usingCreaterOrLower : chr "# Note: A heuristic-based method will be used to assess probe-level differential expression as one of the group sizes is <= 2.\"| __truncated__
..$ usingUserProvided : chr "# Note: Clustering with user-provided function\n"
$ DEMIDiff :List of 12
..$ zeroTargetsFound : chr "0 specified targets were found in the experiment"
..$ calcDiffExp : chr "# Calculating differential expression "
..$ betweenGroups :function (groupA, groupB)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 96 21 96 178 49 206 96 96
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ onUserDefined : chr "on user-defined clusters\n"
..$ analyzingClusterNative:function (clusterName, groupA, groupB)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 98 30 98 246 58 274 98 98
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ analyzingClusterCustom:function (clusterName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 99 30 99 135 58 163 99 99
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ calcHyperGeo : chr "\t\tCalculating hypergeometric distribution p-values ... "
..$ annotatingResults : chr "\t\tAnnotating results ..."
..$ multipleCorrectionBH : chr "\t\tAdjusting p-values for multiple testing by the FDR method (Benjamini & Hochberg, 1995) ... "
..$ multipleCorrectionBY : chr "\t\tAdjusting p-values for multiple testing by the FDR method under dependence (Benjamini & Yekutieli, 2001) ... "
..$ multipleCorrectionBONF: chr "\t\tAdjusting p-values for multiple testing by the Bonferroni method ... "
..$ diffExpDone : chr "# Calculating differential expression ... DONE\n"
$ DEMIExperiment :List of 31
..$ invalidWhatChooseFrom :function (what, chooseFrom)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 112 29 112 188 57 216 112 112
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ notFolder :function (parameter)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 113 17 113 91 45 119 113 113
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ folderEmpty :function (parameter)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 114 19 114 130 47 158 114 114
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ notACELFile :function (file, parameter)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 115 19 115 135 47 163 115 115
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ maxprobesError : chr "The parameter 'maxprobes' has to be a positive integer or set as 'median', 'max' or not defined at all which by default set's i"| __truncated__
..$ probesExcluded :function (excludedProbes)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 117 22 117 195 50 223 117 117
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ noTargetsFound : chr "No targets were found"
..$ noProbesMeasuring : chr "No probes measuring the specified targets matched the experiment criteria"
..$ attachErrorResultsExists:function (variable)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 120 32 120 288 60 316 120 120
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ attachErrorDiffDEMIExp : chr "Can't add results of class 'DEMIDiff' to this experiment of class 'DEMIExperiment' because they represent different 'DEMIExperi"| __truncated__
..$ loadingCEL : chr "# Loading CEL files and creating expression matrix\n"
..$ includedCELFiles :function (celfiles)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 123 24 123 115 52 143 123 123
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ usingMicroarrayPlatform :function (platform)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 124 31 124 120 59 148 124 124
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ libraryNotInstalled :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 125 27 125 114 55 142 125 125
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ searchingInternetRepo :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 126 29 126 142 57 170 126 126
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ packageNotFoundFromRepo :function (packageName, package_url)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 127 31 127 143 59 171 127 127
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ installingPackage :function (packageName, repository)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 128 25 128 142 53 170 128 128
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ checkYourInternet : chr "The current operation could not access the internet. Please check your internet connectction"
..$ loadingAnnoSuccess :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 130 26 130 133 54 161 130 130
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ loadingAnnoFail :function (annoTableName, packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 131 23 131 179 51 207 131 131
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ sectionsizeNotAvail :function (sectionsizes)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 132 27 132 169 55 197 132 132
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ cantLoadWhatTable :function (whatTable)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 133 25 133 116 53 144 133 133
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ loadingBlatSuccess :function (packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 134 26 134 132 54 160 134 134
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ blatDoesNotExists :function (blat, platform, packageName)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 135 25 135 192 53 220 135 135
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ pmsizeNotAvail :function (pmsizes)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 136 22 136 182 50 210 136 136
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ ignoreStrandMatches :function (strand)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 137 27 137 112 55 140 137 137
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ loadingCytoband : chr "# Loading cytoband information\n"
..$ loadingPathway : chr "# Loading pathway information\n"
..$ check4probeError :function (difference)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 140 24 142 124 52 173 140 142
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ check4targetError :function (notfound)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 143 25 143 181 53 209 143 143
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
..$ zeroTargetsFound : chr "0 specified targets were found in the experiment"
$ DEMIResults :List of 2
..$ resultsContain : chr "the results list can only contain objects of class 'DEMIResult'"
..$ resultsUndefined: chr "no results have been defined"
$ diffexp :List of 2
..$ matchesCluster: chr "\t\tCalculating matches for probes in cluster ... "
..$ matchesAll : chr "\t\tCalculating matches over all probes ... "
$ normalization :List of 3
..$ main : chr "# Normalizing expression values "
..$ normrrank : chr " - using 'relative rank' as the normalization method\n"
..$ normquantile: chr "- using 'quantile normalization' as the normalization method\n"
$ parameterMissing :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 171 22 171 93 36 107 171 171
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ parameterNotOfClass :function (parameter, cls)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 172 25 172 116 39 130 172 172
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ isNotError :function (parameter, what)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 173 16 173 93 30 107 173 173
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ hasToBeNumericBetween :function (parameter, start, end)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 174 27 174 142 41 156 174 174
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ tooManyParameters :function (parameter, len)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 175 23 175 111 37 125 175 175
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ positiveInteger :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 176 21 176 106 35 120 176 176
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ positiveIntegerUpTo :function (parameter, to)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 177 25 177 124 39 138 177 177
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ hasToBeFunction :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 178 21 178 98 35 112 178 178
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ notEmptyString :function (parameter)
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 179 20 179 101 34 115 179 179
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ done :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 180 10 180 32 24 46 180 180
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
$ demiStart :function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 184 15 195 111 29 139 184 195
.. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7f8e9424f740>
|
Author(s)
Sten Ilmjarv, Hendrik Luuk
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