read.short.arachne.tags: Read in ARACHNE short tags
In spp: ChIP-Seq Processing Pipeline

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Read in short arachne reads

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

`filename`	filename
`fix.chromosome.names`	Fix chromosome names

Not necessary

A list like structure

No Notes

Peter Kharchenko

spp by Peter Kharchenko

Nothing to see here

## 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", path.expand(filename)), 
        function(d) {
            xo <- order(abs(d$t))
            d$t <- d$t[xo]
            d$n <- d$n[xo]
            return(d)
        })
    if (fix.chromosome.names) {
        names(tl) <- gsub("\.fa", "", names(tl))
    }
    return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl, 
        function(d) d$n)))
  }

## End(Not run)