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1 \name{get.conservative.fold.enrichment.profile}
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2 \alias{get.conservative.fold.enrichment.profile}
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3 %- Also NEED an '\alias' for EACH other topic documented here.
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4 \title{ Estimate minimal fold enrichment/depletion along the chromosomes }
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5 \description{
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6 The method provides a statistical assessment of enrichment/depletion
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7 along the chromosomes. To assess tag density enrichment/depletion, a
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8 sliding window of a specified size (\code{fws}) is used to calculate
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9 the density of the foreground tags (\code{ftl}). Multiple, typically
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10 larger windows are used to estimate background tag (\code{btl}) density around the
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11 same location. The densities are compared as ratios of two Poisson
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12 processes to estimate lower bound of foreground enrichment, or upper
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13 bound of foreground depletion. If multiple window sizes were used to
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14 estimate the background tag density, the most conservative one is
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15 chosen for each point.
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16 }
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17 \usage{
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18 get.conservative.fold.enrichment.profile(ftl, btl, fws, bwsl = c(1, 5, 25, 50) * fws, step = 50, tag.shift = 146/2, alpha = 0.05, use.most.informative.scale = F, quick.calculation = T)
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19 }
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20 %- maybe also 'usage' for other objects documented here.
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21 \arguments{
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22 \item{ftl}{ foreground tag vector list }
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23 \item{btl}{ background tag vector list }
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24 \item{fws}{ foreground window size }
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25 \item{bwsl}{ background window scales. The size(s) of background windows
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26 will be \code{fws*bwsl}. }
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27 \item{step}{ spacing between positions at which the
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28 enrichment/depletion is evaluated }
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29 \item{tag.shift}{ number of basepairs by which positive and negative
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30 tag coordinates should be shifted towards eachother (half of binding
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31 peak separation distance)}
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32 \item{alpha}{ desired level of statistical significance }
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33 \item{use.most.informative.scale}{ for each position, instead of
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34 evaluating enrichment ratio bounds for all background window scales,
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35 choose the one with the highest observed density to speed up the calculations}
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36 \item{quick.calculation}{ Use square root transformation method
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37 instead of a Bayesian method. This speeds up the caclulation
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38 considerably and is turned on by default. }
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39 \item{background.density.scaling}{ If TRUE, regions of significant tag
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40 enrichment will be masked out when calculating size ratio of the
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41 signal to control datasets (to estimate ratio of the background tag
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42 density). If FALSE, the dataset ratio will be equal to the ratio of
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43 the number of tags in each dataset.}
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44 }
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45 \value{
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46 A list of elements corresponding to chromosomes, with each element
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47 being an $x/$y data.frame giving the position and the log2
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48 conservative estimate of enrichment/depletion fold ratios around that
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49 position.
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50 Use \code{\link{writewig}} to output the structure to a WIG
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51 file.
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52 }
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53 \references{ R.M.Price, D.G. Bonett "Estimating the ratio fo two Poisson
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54 rates", Comp. Stat & Data Anal. 32(2000) 345}
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55 \seealso{ \code{\link{get.smoothed.tag.density}} }
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56 \examples{
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57 enrichment.estimates <- get.conservative.fold.enrichment.profile(chip.data,input.data,fws=2*binding.characteristics$whs,step=100,alpha=0.01);
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58 writewig(enrichment.estimates,"example.enrichment.estimates.wig","Example conservative fold-enrichment/depletion estimates shown on log2 scale");
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59 }
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