Dumping data from R to a text file (June 27, 2005). Category: Data management

In the prenatal liver study, I needed to give some of the normalized gene expression levels to a researcher in a form he could use. The data he needed was in a data frame with 94 rows and 16 columns (folate.signal). But unfortunately, the names of the rows (gene.symbol) and columns (liver.names) were stored in separate objects. Here's one way to match the values back up.

First, there are duplicates in the gene.symbol list, so to create new names, use the makeUnique function found in the limma library. Then change folate.signal from a data frame to a matrix. Use the dimnames function to add the row and column names to the matrix. Finally, use the write.table function to create a text file.

gene.unique <- makeUnique(paste(gene.symbol," "))
folate.matrix <- as.matrix(folate.signal)
dimnames(folate.matrix) <- list(gene.unique,liver.names)

This page was written by Steve Simon while working at Children's Mercy Hospital. Although I do not hold the copyright for this material, I am reproducing it here as a service, as it is no longer available on the Children's Mercy Hospital website. Need more information? I have a page with general help resources. You can also browse for pages similar to this one at