dfs2one: Combine multiple expression tables (.tsv) into a single data...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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")

almeidasilvaf/BioNERO documentation built on March 25, 2024, 9:14 p.m.