get.conservative.fold.enrichment.profile2: Return Conservative fold enrichment profile controlling for...

In spp: ChIP-Seq Processing Pipeline

Description

Returns a conservative upper/lower bound profile (log2) given signal tag list, background tag list and window scales controlling for input, and supporting only a single background scale.

Novel version of get.conservative.fold.enrichment.profile() supporting a single background scale.

Usage

get.conservative.fold.enrichment.profile2(ftl1, ftl2, btl1, btl2, fws,
           bws = 1 * fws, step = 50, tag.shift = 146/2, 
           alpha = 0.05, background.density.scaling = T,
           bg.weight1 = NULL, bg.weight2 = NULL, 
           posl = NULL, return.mle = F)

Arguments

ftl1	Parameter
ftl2	Parameter
btl1	Parameter
btl2	Parameter
fws	Parameter
bws	Parameter
step	Parameter
tag.shift	Parameter
alpha	Parameter
background.density.scaling	Parameter
bg.weight1	Parameter
bg.weight2	Parameter
posl	Parameter
return.mle	Parameter

Value

A list of elements corresponding to chromosomes, with each element being an $x/$y data.frame giving the position and associated log2 signal/control enrichment estimate.

See Also

get.smoothed.enrichment.mle

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 (ftl1, ftl2, btl1, btl2, fws, bws = 1 * fws, step = 50, 
    tag.shift = 146/2, alpha = 0.05, background.density.scaling = T, 
    bg.weight1 = NULL, bg.weight2 = NULL, posl = NULL, return.mle = F) 
{
    ftl1 <- ftl1[unlist(lapply(ftl1, length)) > 2]
    chrl <- names(ftl1)
    names(chrl) <- chrl
    if (!is.null(posl)) {
        chrl <- chrl[chrl %in% names(posl)]
    }
    if (is.null(bg.weight1)) {
        bg.weight1 <- dataset.density.ratio(ftl1, btl1,
                      background.density.scaling = background.density.scaling)
    }
    if (is.null(bg.weight2)) {
        bg.weight2 <- dataset.density.ratio(ftl2, btl2,
                      background.density.scaling = background.density.scaling)
    }
    lapply(chrl, function(chr) {
        x <- binomial.proportion.ratio.bounds(abs(ftl1[[chr]] + 
            tag.shift), abs(btl1[[chr]] + tag.shift), abs(ftl2[[chr]] + 
            tag.shift), abs(btl2[[chr]] + tag.shift), fws = fws, 
            bws = bws, step = step, bg.weight1 = bg.weight1, 
            bg.weight2 = bg.weight2, alpha = alpha, pos = if (is.null(posl)) {
                NULL
            }
            else {
                posl[[chr]]
            })
        ps <- rep(0, length(x$mle))
        vi <- which(!is.na(x$lb) & x$lb > 0)
        ps[vi] <- x$lb[vi]
        vi <- which(!is.na(x$ub) & x$ub < 0)
        ps[vi] <- x$ub[vi]
        if (is.null(posl)) {
            if (return.mle) {
                return(data.frame(x = x$x, y = ps, mle = x$mle, 
                  lb = x$lb, ub = x$ub))
            }
            else {
                return(data.frame(x = x$x, y = ps))
            }
        }
        else {
            if (return.mle) {
                return(data.frame(x = posl[[chr]], y = ps, mle = x$mle, 
                  lb = x$lb, ub = x$ub))
            }
            else {
                return(data.frame(x = posl[[chr]], y = ps))
            }
        }
    })
  }

## End(Not run)

spp documentation built on May 30, 2019, 5:03 p.m.