12IlluminaSeriesTXTilluminaNonNormalizedfalsetruefalseIllumina Non-NormalizedlinesCount0skipLines0firstLineheaderCheckLinelineElemsfalseSets the first linecommentCommentComentário{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 Sets the first line\par } DefinitionDefiniçãofalseDefine Definir valor falseGets the text from line Obtém texto da linha falseValue1truefalse. . trueNote: First line starts from index 1Nota: A primeira linha é a de índice 1trueNote: If this is not a text file or is a binary archive, this evaluation may give unexpected resultsNota: Se o arquivo não for textual ou estiver em formato binário, esta operação pode levar a resultados inesperadosfalselinetextLine AtLinha emfalseReferencefalse for para trueVariablefalsesettextvarTextTextofalseIf the line starts with this sentence below, it is possible that the first line in table is after the first line in the file{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 If the line starts with this sentence below, it is possible that the first line in table is after the first line in the file\par } ValueValorfalseValor falsefalseVariablecontaintextposText locationLocal do textofalseValue1falseValue# The identifiers in the ID_REF column must match the identifiers in the ID columnfalse, considering , considerando capitalsCharacter CasingMaiúsculas e MinúsculasfalseValue0falsetextcontainsText contains TextTexto contém TextofalseReferencefalsefalse is true? é verdadeiro? istrueIs True?Verdadeiro?DataDadosfalseStarts reading the current file from the line Lê arquivo atual a partir da linha falseValue1truefalse. Then, reads , lendo até um total de falseValue10falsefalse lines, where each line is stored in linhas, e para cada linha armazenada em trueVariablefalse and propagates the following actions. , realiza ações subsequentes. trueNote: Number 1 is the index for the first lineNota: A primeira linha é a de índice 1falsereadlinecountRead N LinesLer N linhasfalsefalseValue^[^\t\r\n]*?ID[^\t\r\n]*?(?:\t[^\t\r\n]+?\t[^\t\r\n]*?Detection\sPval)+$None-10000^·^·t·r·n··�ID·^·t·r·n··�(�··t·^·t·r·n·+�·t·^·t·r·n··�Detection·sPval)+$false matches for input encontra resultados para falseVariablefalse Note: The last captures are stored in the regular expression variable. Nota: Últimas correspondências são armazenadas na própria expressão regular. regexmatchPattern MatchesPadrão correspondefalseReferencefalseLoopCiclofalseIncreases the value from Incrementa em 1 o valor de trueVariable0falsefalse by 1 intincIncrease IntegerIncrementar InteirofalseVariabletrueVariablefalseExits the current loop, resuming the actions outside the loop. Sai do ciclo atual, prosseguindo com as ações fora deste ciclo. exitcycleExit LoopSair do Ciclo AtualfalseVerifies if the first line has pairs of expression values and p-values{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 Verifies if the first line has pairs of expression values and p-values\par } falseValue^[^\t\r\n]*?ID[^\t\r\n]*?(?:\t[^\t\r\n]+?\t[^\t\r\n]*?Detection\sPval)+$None-10000^·^·t·r·n··�ID·^·t·r·n··�(�··t·^·t·r·n·+�·t·^·t·r·n··�Detection·sPval)+$falseVariablefalseReferencefalseR EnvironmentRfalseRuns the following R command: Executa o seguinte comando no R: falseConcatenates Reúne falseValueskipLines <- false and e falseConvert Converte falseVariable0falsefalse to text. para texto. inttotextInteger to TextInteiro para textofalseReferencefalse into a single text. em um único texto. concatConcatenate TextConcatenar textofalseReferencefalserunrscriptRun R CommandExecutar Comando no RfalseIf so, reads as a table of expression and p-values{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 If so, reads as a table of expression and p-values\par } ProgressProgressofalseUpdate progress message to Atualizar progresso para falseValue5truefalse%, printing the message %, com mensagem falseValueReading the first linesfalseprogressmessageandpercentMessage and PercentageMensagem e PorcentagemfalseReads the current file starting from the line Lê arquivo atual a partir da linha falsefalseValue2falseoperatorArithmetic OperatorOperador MatemáticofalseValue0falseVariable0falsefalseintarithmeticArithmetic OperationOperação aritméticafalseReference1truefalse, treating each line as a table row como tabela readtableoptionsTable Reading OptionsOpções de Leitura de TabelafalseValue0false For each row, splits the values in cells from cell Para cada linha, separar os valores em células a partir da célula falseValue2truefalse onwards, storing the values in , armazenando estes valores em trueVariablelineValuesfalse If present, replace invalid values to Para valores inválidos, substituir por constnanNaNNaNfalseReference0falsetrueNote: Number 1 is the index for the first lineNota: A primeira linha é a de índice 1trueNote: The first cell is cell 1Nota: A primeira célula é a célula 1falsereadnumtableRead Table (Numeric)Ler Tabela NuméricafalsefalseReference0falsefalse is included in está dentro da lista falseVariablefalseinlistnumList ContainsLista contém valorfalseReferencefalsetrueVariable0falsefalsefalseVariable0falsecompareArithmetic ComparisonComparação Entre ValoresfalseValue2falseValue51falsefalsecompareintCompare IntegersComparar inteirosfalseReferencefalsefalseIf there are NaN values, finalizes the checking without validating the file.{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 If there are NaN values, finalizes the checking without validating the file.\par } RuntimeExecuçãofalseConcludes the file checking and skips any further file checking in the current session. Conclui checagem deste arquivo e não executa qualquer ação subsequente returnFinalizeConcluirfalseLet's say that at least 50 data lines are needed to validate this file.{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 Let's say that at least 50 data lines are needed to validate this file.\par } falseVariable0falsefalseValue2falseValue50falsefalseReferencefalsefalseIn this step, the probe names will be stored, thus related dependencies can be identified.{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 In this step, the probe names will be stored, thus related dependencies can be identified.\par } falseDefine Definir valor falseValue0falsefalse for para trueVariable0falsefalsesetintvarInteger ValueNúmero InteirofalseValue50truefalseValueStoring the probe namesfalseReads the current file starting from the line Lê arquivo atual a partir da linha falsefalseVariable0falseoperatorArithmetic OperatorOperador MatemáticofalseValue0falseValue2falsefalseintarithmeticArithmetic OperationOperação aritméticafalseReference2truefalse, treating each line as a table row como tabela readtableoptionsfalseValue0false. For each row, stores the cells in . Cada linha é dividida em células, as quais são armazenadas em trueVariabletrueNote: Number 1 is the index for the first lineNota: A primeira linha é a de índice 1falsereadtableRead Table (Text)Ler TabelaListsListasfalseAdd Adiciona falseElement Elemento bem listendList End LocationPosição na ListafalseValue1false of de falseVariabletrueIf the list has no elements, returns an empty text.Se a lista não possuir elementos, retorna um texto vazio.falseendelementoElement At EndElemento finalfalseReferencefalse at logo listendfalseValue0false for da lista falseProbe identifiers list of type Lista de identificadores de sonda do tipo probeidtypeProbe Identifier TypeTipo de Identificadores de SondafalseValue0trueNote: For performance reasons, the items order is not guaranteed in Probe Names and Array Probe IDs.Nota: Por razões de performance, a ordem dos itens não é garantida para Nomes e IDs físicos de sonda.falseprobeidlistProbe IdentifiersIdentificadores de sondafalseReferencefalseaddtolistAdd to ListAdicionar à listatrueVariable0falsefalseValue90truefalseValueFinalizingfalseAfter listing the probe names, these probes can match to probe names from platform files, grouping the files in a common dependency.{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 After listing the probe names, these probes can match to probe names from platform files, grouping the files in a common dependency.\par } ValidationValidaçãofalseDefines a new dependency for this file. Group name: Adiciona nova dependência para este arquivo. Nome do grupo: falseValueIllumina GSEfalse Is mandatory: Dependência obrigatória: falseValuefalsefalse Depends on data type: Tipo de dados a depender: filetypeFile Data TypeTipo de Arquivo de DadosfalseValue3false Solves dependency by matching: Resolver dependência por: dependencytypeDependency TypeTipo de DependênciafalseValue1false After solving a dependency: Após dependência resolvida: dependencyaftersolveAfter Solving DependencyApós Resolver DependênciafalseValue0falsedependencyaddAdd DependencyAdicionar DependênciafalseTransfers the line count to attached info. This data can be accessed during treatment.{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 Transfers the line count to attached info.\par \pard This data can be accessed during treatment.\par } DataDadosfalseAdds or updates an info named Adiciona ou atualiza informação de nome falseValuelinesCountfalse with the value para o valor falseVariable0falsefalseReferencefalseattachinfoAttach InfoAnexar InformaçãofalseFinal and essential step: Mark file as valid{\rtf1\ansi\ansicpg1252\deff0\deflang1046{\fonttbl{\f0\fnil\fcharset0 Lucida Console;}} {\colortbl ;\red64\green64\blue64;} \viewkind4\uc1\pard\cf1\f0\fs18 Final and essential step: Mark file as valid\par } falseValidates the file to Valida arquivo como falseValuetruetrue Note: TRUE for validated and FALSE to invalid file Nota: TRUE para validado e FALSE para arquivo inválido falsevalidatefileValidate FileValidar arquivo0falsefilterPValuesfalsefalseFilter P-ValuestrueLess than 0.05Less than 0.010trueremoveRowswithPValuesfalsetrueRemove Rows with P-ValuestrueNoneNormal+Exponential Convolution (normexp)0falsebackgroundCorrectionfalsetrueBackground CorrectiontrueSaddleMLERMARMA751truenormExpMethodfalsetrueNormExp MethodtrueScaleQuantilesCyclic LowlessNone0falsenormalizationMethodfalsetrueNormalization MethodtrueFastAffymetrix (affy)Pairs2truecyclicMethodfalsetrueCyclic 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 with P-ValuesSeriesExpressionSet# Loads auxiliary functions giveStatus = rgeap:::.give.status # Reads the text table giveStatus(10, 'Lendo tabela', 'Reading table') linesToSkip <- as.integer(skipLines) m <- read.table(file = inputFiles[1], header = 1, row.names = 1, sep = '\t', check.names = F, skip = linesToSkip) # Extracts only the values arrayVals <- m[,(1:(ncol(m)/2))*2 - 1] # If p-value filtering is enabled if (filterPValues) { giveStatus(50, 'Filtrando valores', 'Filtering values') # Gets the removeRowswithPValues option according to the index if (removeRowswithPValues == 1) lessthanpar <- 0.05 else lessthanpar <- 0.01 arrayVals <- m[,(1:(ncol(m)/2))*2 - 1] # Extracts the p-values pVals <- m[,(1:(ncol(m)/2))*2] # Gets only the lines with all p-values less than the parameter pValSatisfied <- sapply(X = 1:nrow(pVals), FUN = function(i) all(pVals[i,] < lessthanpar)) # Filters the rows with relevant p-values m <- arrayVals[pValSatisfied,] } else { m <- m[,(1:(ncol(m)/2))*2 - 1] } #Applying treatment methods giveStatus(75, 'Aplicando tratamento estatístico', 'Applying statistical treatment') bgMethod <- c('none', 'normexp')[backgroundCorrection + 1] neMethod <- c('saddle', 'mle', 'rma', 'rma75')[normExpMethod + 1] normMethod <- c('scale', 'quantile', 'cyclicloess', 'none')[normalizationMethod + 1] cycMethod <- c('fast', 'affy', 'pairs')[cyclicMethod + 1] # Make statistical treatment m <- as.matrix(m) m <- treat.limma(m, bg.method = bgMethod, bg.normexp.method = neMethod, norm.method = normMethod, norm.cyclic.method = cycMethod) remove('skipLines') giveStatus(90, 'Finalizando', 'Concluding') # Finally, convert back to ExpressionSet (see Properties => Treated R Object) SeriesExpressionSet <- df.to.eset(m)