sort some Galaxy-downloaded BED format

sort_my_bed.R

names(galaxy_bed) <- c("chrom",
  "chromStart",
  "chromEnd",
  "name",
  "score",
  "strand",
  "blockCount",
  "blockSizes")

# This shows how to 'subset' with either the $ operator or [[

eg_with_square_brackets <- galaxy_bed[["chromStart"]]
eg_with_dollar <- galaxy_bed$chromStart

# The most hassle free way to sort a data frame is to use a package from the community's "tidy data" set of packages,
# like dplyr, tidyr etc.

library(plyr) #load the plyr package, which wraps the order function from base R

# preview the top of the sorted table
head(arrange(galaxy_bed, decreasing=FALSE))

# observe how the decreasing parameter is passed to order by the ellipsis in plyr's arrange function
# see: http://ipub.com/r-three-dots-ellipsis/ etc for description of what the ellipsis does in an R function

head(arrange(galaxy_bed, galaxy_bed$name, decreasing = FALSE))
head(arrange(galaxy_bed, galaxy_bed$name, decreasing = TRUE))