1OtherSamplePAIRnimbleScanPairfalsetruefalseNimbleScan PairlineCount0positionIndex5currentLinecurrCellsMultiple TestsMúltiplos TestesfalsefalsefalseGets 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 emfalseReferencecontaintextposText locationLocal do textofalseValue1falseValue# software=NimbleScanfalse, considering , considerando capitalsCharacter CasingMaiúsculas e MinúsculasfalseValue0falsetextcontainsText contains TextTexto contém TextofalseReferencefalsefalse and e falsefalseValue^IMAGE_ID\tGENE_EXPR_OPTION\tSEQ_ID\tPROBE_ID\tPOSITION\tNone-10000^IMAGE·ID·tGENE·EXPR·OPTION·tSEQ·ID·tPROBE·ID·tPOSITION·tfalse matches for input encontra resultados para falseValue2truefalseReferencefalse Note: The last captures are stored in the regular expression variable. Nota: Últimas correspondências são armazenadas na própria expressão regular. regexmatchPattern MatchesPadrão correspondefalseReferencefalsefalse are both true. são verdadeiras. andAndEDefinitionDefiniçãofalseDefine Definir valor falseValue5falsefalse for para trueVariable0falsefalsesetintvarInteger ValueNúmero InteiroDataDadosfalseReads the current file starting from the line Lê arquivo atual a partir da linha falseValue3truefalse, treating each line as a table row como tabela readtableoptionsTable Reading OptionsOpções de Leitura de TabelafalseValue0false. 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 TabelaValueValorfalseValor falsefalseVariable0falsecompareArithmetic ComparisonComparação Entre ValoresfalseValue2falseValue50falsefalsecompareintCompare IntegersComparar inteirosfalseReferencefalsefalse is true? é verdadeiro? istrueIs True?Verdadeiro?LoopCiclofalseIncreases the value from Incrementa em 1 o valor de trueVariable0falsefalse by 1 intincIncrease IntegerIncrementar InteiroListsListasfalseAdd Adiciona falseElement at index Elemento no índice falseVariable0truefalse from de falseVariablefalse Consider the first item as Considerar primeiro índice como indexbasedFirst Index in this ListPrimeiro Índice nesta ListafalseValue1trueZero-based indexes range from [0] to [Item count minus 1]Índices baseados em zero variam de [0] a [Nº de itens menos 1]trueOne-based indexes range from [1] to [Item count]Índices baseados em um variam de [1] a [Nº de itens]trueOut-of-range indexes will return an empty string.Índices fora de alcance retornarão um texto vazio.falselistelementElement At IndexElemento emfalseReferencefalse at logo listendList End LocationPosição na ListafalseValue0false 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 listaValidationValidaçãofalseValidates 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 arquivofalseDefines a new dependency for this file. Group name: Adiciona nova dependência para este arquivo. Nome do grupo: falseValueNimbleScanPairsfalse 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 DependênciafalseValue1falsedependencyaddAdd DependencyAdicionar DependênciafalseExits the current loop, resuming the actions outside the loop. Sai do ciclo atual, prosseguindo com as ações fora deste ciclo. exitcycleExit LoopSair do Ciclo Atual0falseignoreMismatchPairsfalsefalseIgnore Mismatch Pairstrue0falsecomputeAverageIntensitiesBySEQIDfalsefalseCompute Average Intensities By 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Mismatch FilterSeriesExpressionSet# Simplifies names without path and extension safefilenames <- sub(pattern = '^.*[/\\]([^.]+)[.].*', replacement = '\\1', x = inputFiles) fCount <- length(inputFiles) # Reads the first table of files rgreap:::.give.status(90 / fCount, paste0('Lendo amostras (1 de ', fCount, ')'), paste0('Reading Files (1 of ', fCount, ')') ) m <- read.table(file = inputFiles[1], header = 1, row.names = 4, sep = '\t', skip = 1) pm <- data.frame(row.names = rownames(m)) mm <- data.frame(row.names = rownames(m)) seqIDs <- m$SEQ_ID pm[[safefilenames[1]]] <- m$PM mm[[safefilenames[1]]] <- m$MM # Reads the remaining files if (fCount > 1) { for (i in 2:fCount) { rgreap:::.give.status(90 * i / fCount, paste0('Lendo amostras (', i ,' de ', fCount, ')'), paste0('Reading Files (', i ,' of ', fCount, ')') ) m <- read.table(file = inputFiles[i], header = 1, row.names = 4, sep = '\t', skip = 1) pm[[safefilenames[i]]] <- m$PM mm[[safefilenames[i]]] <- m$MM } } # Process according to treatment options rgreap:::.give.status(95, 'Processando dados e finalizando', 'Processing data and finishing') if (ignoreMismatchPairs) { mmv <- rowSums(mm) mmv <- mmv == 0 if (!all(mmv)) { pm <- pm[mmv,] seqIDs <- seqIDs[mmv] } } if (computeAverageIntensitiesBySEQID) { library('limma') pm <- avereps(x = pm, ID = seqIDs) } SeriesExpressionSet <- df.to.eset(pm)