get.smoothed.enrichment.mle2: Calculate background input controlled chromosome-wide...

In spp: ChIP-Seq Processing Pipeline

Description

Given signal and control tag positions, the method calculates log2 signal to control enrichment esimates (maximum likelihood) for each chromosome, based on the smoothed tag density profile (see get.smoothed.tag.density).

Usage

get.smoothed.enrichment.mle2(signal.tags1, control.tags1,
                             signal.tags2, control.tags2,
                             tag.shift = 146/2, background.density.scaling = F,
                             pseudocount = 1, bg.weight1 = NULL,
                             bg.weight2 = NULL,
                             rngl = NULL, chrl = NULL, ...)

Arguments

signal.tags1	Parameter
control.tags1	Parameter
signal.tags2	Parameter
control.tags2	Parameter
tag.shift	Parameter
background.density.scaling	Parameter
pseudocount	Parameter
bg.weight1	Parameter
bg.weight2	Parameter
rngl	Parameter
chrl	Parameter
...	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 (signal.tags1, control.tags1, signal.tags2, control.tags2, 
    tag.shift = 146/2, background.density.scaling = F, pseudocount = 1, 
    bg.weight1 = NULL, bg.weight2 = NULL, rngl = NULL, chrl = NULL, 
    ...) 
{
    if (is.null(chrl)) {
        chrl <- intersect(names(signal.tags1), names(signal.tags2))
        names(chrl) <- chrl
    }
    if (is.null(rngl)) {
        rngl <- lapply(chrl, function(chr) range(c(range(abs(signal.tags1[[chr]] + 
            tag.shift)), range(abs(signal.tags2[[chr]] + tag.shift)))))
    }
    else {
        chrl <- names(rngl)
        names(chrl) <- chrl
    }
    ssd1 <- get.smoothed.tag.density(signal.tags1, rngl = rngl, 
        ..., scale.by.dataset.size = F)
    ssd2 <- get.smoothed.tag.density(signal.tags2, rngl = rngl, 
        ..., scale.by.dataset.size = F)
    csd1 <- get.smoothed.tag.density(control.tags1, rngl = rngl, 
        ..., scale.by.dataset.size = F)
    csd2 <- get.smoothed.tag.density(control.tags2, rngl = rngl, 
        ..., scale.by.dataset.size = F)
    if (is.null(bg.weight1)) {
        bg.weight1 <- dataset.density.ratio(signal.tags1, control.tags1, 
            background.density.scaling = background.density.scaling)
    }
    if (is.null(bg.weight2)) {
        bg.weight2 <- dataset.density.ratio(signal.tags2, control.tags2, 
            background.density.scaling = background.density.scaling)
    }
    cmle <- lapply(chrl, function(chr) {
        d <- ssd1[[chr]]
        d$y <- log2(ssd1[[chr]]$y + pseudocount * bg.weight1) - 
            log2(csd1[[chr]]$y + pseudocount) - log2(bg.weight1) - 
            log2(ssd2[[chr]]$y + pseudocount * bg.weight2) + 
            log2(csd2[[chr]]$y + pseudocount) + log2(bg.weight2)
        return(d)
    })
  }

## End(Not run)

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