summarize: A script to generate summarize statistics from input

summarize

#!/usr/bin/Rscript
#
# Quickly generate some basic descriptive
# statistics from stdin
#

library('optparse', quietly=TRUE)


option_list <- list(make_option(c("-H", "--header"), action="store_true", default=FALSE,
                                help="Use first line of input as headers."),
                    make_option(c("-r", "--rownames"), action="store", default=NULL,
                                help="Column to use as row names."),
                    make_option(c("-s", "--sep"), action="store", default="",
                                 help="Column seperator. Defaults to white space"))
parser <- OptionParser(usage = "%prog [OPTIONS] [FILE]", option_list=option_list)

arguments <- parse_args(parser, positional_arguments=TRUE)
opts <- arguments$options
args <- arguments$args

input_file <- if (is.na(args[1])) {
  file('stdin')
} else {
  args[1]
}

input <- read.table(input_file, header=opts$header, sep=opts$sep, row.names=opts$rownames)

summary(input)

write("\nCovariance Matrix:", stdout())
var(input)

write("\nColumn Sums:", stdout())
colSums(input)

write("\nNumber of Rows:", stdout())
nrow(input)

write("\nFirst 6 Rows:", stdout())
head(input)