read.helicos.tags: Read in helicos tags
In hms-dbmi/spp: ChIP-Seq Processing Pipeline

Description Usage Arguments Value See Also Examples

Read in Helicos tags

1 2	read.helicos.tags(filename, read.tag.names = F, fix.chromosome.names = F, include.length.info = T)

`filename`	filename
`read.tag.names`	Read in tag names
`fix.chromosome.names`	Do we fix chromosome names
`include.length.info`	include length information

A list like structure

Fill in later

## 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, read.tag.names = F, fix.chromosome.names = F, 
    include.length.info = T) 
{
    if (read.tag.names) {
        rtn <- as.integer(1)
    }
    else {
        rtn <- as.integer(0)
    }
    tl <- lapply(.Call("read_helicostabf", path.expand(filename), 
        rtn), function(d) {
        xo <- order(abs(d$t))
        d$t <- d$t[xo]
        d$n <- d$n[xo]
        d$l <- d$l[xo]
        if (read.tag.names) {
            d$s <- d$s[xo]
        }
        return(d)
    })
    if (fix.chromosome.names) {
        names(tl) <- gsub("\.fa", "", names(tl))
    }
    if (read.tag.names) {
        return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl, 
            function(d) d$n), length = lapply(tl, function(d) d$l), 
            names = lapply(tl, function(d) d$s)))
    }
    else {
        return(list(tags = lapply(tl, function(d) d$t), quality = lapply(tl, 
            function(d) d$n), length = lapply(tl, function(d) d$l)))
    }
  }

## End(Not run)