dfs2one {BioNERO} | R Documentation

## Combine multiple expression tables (.tsv) into a single data frame

### Description

This function reads multiple expression tables (.tsv files) in a directory and combines them into a single gene expression data frame.

### Usage

    dfs2one(mypath, pattern = ".tsv$")

### Arguments

`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.

### Value

Data frame with gene IDs as row names and their expression values in each sample (columns).

### Author(s)

Fabricio Almeida-Silva

### Examples

    # 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")

[Package BioNERO version 1.0.4 Index]