AverageMatrices.R

#!/usr/bin/env Rscript

# Perform cell-wise averaging of matrices (ignoring headers and row names)

# Standard install if missing
list.of.packages <- c("argparse", "abind")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
for(i in list.of.packages){suppressMessages(library(i, character.only = TRUE))}


# Parse commandline arguments
parser <- ArgumentParser()
parser$add_argument('-i',
                    '--infiles',
                    nargs='+',
                    required=TRUE,
                    help="All the matrices to average.")
parser$add_argument('-s',
                    '--separator',
                    action='store',
                    default='\t',
                    help='The field separator for the input matrices (they should all match). [Def = \t].')
parser$add_argument('-o',
                    '--outfile',
                    action='store',
                    required=TRUE,
                    help='Output file to store the averaged matrix in.')

args <-parser$parse_args()

cat("Averaging the following matrices:", "\n")
cat("=================================", "\n")
args$infiles

cat("Outputting to:", "\n")
cat("==============", "\n")
args$outfile

# Read tables in from argument list
cat("Made tables...", "\n")
tables <- lapply(args$infiles, read.table, header=TRUE, row.names=1, check.names=FALSE, sep=args$sep)

# Convert to matrices
cat("Made matrices...", "\n")
matrices <- lapply(tables, as.matrix)

# 'Vertically' bind the matrices. Think of it as a z-stack of matrices.
cat("Vertically binding arrays...", "\n")
stack <- abind(matrices, along=3)

# Average them
stack_avg <- apply(stack, c(1,2), mean)

# Write file
write.table(stack_avg, args$outfile, sep=args$sep, col.names = NA, quote = FALSE)
cat("File written to: ", "\n", args$outfile, "\n")