spp (version 1.16.0)

read.arachne.tags: Read in Arachne tags

Description

Read in ARACHNE Tag file

Usage

read.arachne.tags(filename, fix.chromosome.names = F)

Arguments

filename

filename

fix.chromosome.names

do we fix chromosome names

Value

A list like element

See Also

Fill in later

Examples

# NOT RUN {
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (filename, fix.chromosome.names = F) 
{
    tl <- lapply(.Call("read_arachne_long", path.expand(filename)), 
        function(d) {
            xo <- order(abs(d$t))
            d$t <- d$t[xo]
            d$n <- d$n[xo]
            d$l <- d$l[xo]
            return(d)
        })
    if (fix.chromosome.names) {
        names(tl) <- gsub("\.fa", "", names(tl))
    }
    return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl, 
        function(d) d$n), length = lapply(tl, function(d) d$l)))
  }
# }