dfs2one {BioNERO} | R Documentation |
This function reads multiple expression tables (.tsv files) in a directory and combines them into a single gene expression data frame.
dfs2one(mypath, pattern = ".tsv$")
mypath |
Path to directory containing .tsv files. Files must have the first column in common, e.g. "Gene_ID". Rows are gene IDs and columns are sample names. |
pattern |
Pattern contained in each expression file. Default is '.tsv$', which means that all files ending in '.tsv' in the specified directory will be considered expression files. |
Data frame with gene IDs as row names and their expression values in each sample (columns).
Fabricio Almeida-Silva
# Simulate two expression data frames of 100 genes and 30 samples genes <- paste0(rep("Gene", 100), 1:100) samples1 <- paste0(rep("Sample", 30), 1:30) samples2 <- paste0(rep("Sample", 30), 31:60) exp1 <- cbind(genes, as.data.frame(matrix(rnorm(100*30),nrow=100,ncol=30))) exp2 <- cbind(genes, as.data.frame(matrix(rnorm(100*30),nrow=100,ncol=30))) colnames(exp1) <- c("Gene", samples1) colnames(exp2) <- c("Gene", samples2) # Write data frames to temporary files tmpdir <- tempdir() tmp1 <- tempfile(tmpdir = tmpdir, fileext = ".exp.tsv") tmp2 <- tempfile(tmpdir = tmpdir, fileext = ".exp.tsv") write.table(exp1, file=tmp1, quote=FALSE, sep="\t") write.table(exp2, file=tmp2, quote=FALSE, sep="\t") # Load the files into one exp <- dfs2one(mypath = tmpdir, pattern=".exp.tsv")