simplifyResult {InterMineR} | R Documentation |
This function converts the values of a column variable within a dataset into comma-separated, character strings. The process is achieved by using another column of the same dataset as index.
simplifyResult( dataset, index_column, values_column, returnInDataframe = FALSE )
dataset |
a data.frame containing the data |
index_column |
a character string or a numeric/integer value indicating the column which will be used as index. |
values_column |
a character string or a numeric/integer value indicating the column whose values will be converted into comma-separated, character strings. |
returnInDataframe |
a logical value indicating whether to return only the converted columns or to append the character strings to the dataset. |
If returnInDataframe argument is set to FALSE then a data.frame is returned with the unique values of the index column and the character strings of the values_column that correspond to each.
If returnInDataframe argument is set to TRUE then the original dataset is returned containing an extra column in which the character strings of the values_column have been appended.
InterMine Team
# get HumanMine im.human = initInterMine(listMines()["HumanMine"]) # get template query for retrieving GOTerms for specific genes qGene_GO = getTemplateQuery(im.human, "Gene_GO") # retrieve GOTerms for four different genes rGene_GO = list(NULL) for(i in seq(length(c("PPARG", "RPL5", "RPL11", "TP53")))){ g = c("PPARG", "RPL5", "RPL11", "TP53")[i] qGene_GO$where[[1]]$value = g rGene_GO[[i]] = runQuery(im.human, qGene_GO) } # rbind results to data.frame rGene_GO = do.call(rbind, rGene_GO) # return simplified GOTerms results for each Gene simplify_GOTerms = simplifyResult( dataset = rGene_GO, index_column = "Gene.symbol", values_column = "Gene.goAnnotation.ontologyTerm.identifier", returnInDataframe = FALSE ) # return simplified GOTerms results for each Gene, within the original data.frame simplify_GOTerms.2 = simplifyResult( dataset = rGene_GO, index_column = "Gene.symbol", values_column = "Gene.goAnnotation.ontologyTerm.identifier", returnInDataframe = TRUE )