read.tagalign.tags: Read in tagalign tags
In spp: ChIP-Seq Processing Pipeline

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

Fill in later

1	read.tagalign.tags(filename, fix.chromosome.names = T, fix.quality = T)

`filename`	Filename of tag file
`fix.chromosome.names`	chromosome names
`fix.quality`	fix quality

...

a list like structure

Needs further editing

Peter K.

spp by kharchenko

Buh!

## 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 = T, fix.quality = T) 
{
    tl <- lapply(.Call("read_tagalign", path.expand(filename)), 
        function(d) {
            xo <- order(abs(d$t))
            d$t <- d$t[xo]
            d$n <- d$n[xo]
            if (fix.quality) {
                if (min(d$n) < 0.5) {
                  d$n = ceiling(1000/4^d$n)
                }
                break.vals <- unique(sort(c(0, unique(d$n))))
                d$n <- length(break.vals) - 1 - cut(d$n, breaks = break.vals, 
                  labels = F)
            }
            return(d)
        })
    if (fix.chromosome.names) {
        names(tl) <- gsub("\.fa", "", names(tl))
    }
    return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl, 
        function(d) d$n)))
  }

## End(Not run)