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6
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1 \name{get.binding.characteristics}
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2 \alias{get.binding.characteristics}
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3 %- Also NEED an '\alias' for EACH other topic documented here.
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4 \title{ Calculate characteristics of observed DNA-binding signal from
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5 cross-correlation profiles }
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6 \description{
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7 The methods calculates strand cross-correlation profile to determine binding
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8 peak separation distance and approximate window size that should be used
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9 for binding detection. If quality scores were given for the tags,
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10 which quality bins improve the cross-correlation pattern.
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11 }
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12 \usage{
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13 get.binding.characteristics(data, srange = c(50, 500), bin = 5, cluster = NULL, debug = F, min.tag.count = 1000, acceptance.z.score = 3, remove.tag.anomalies = T, anomalies.z = 5,accept.all.tags=F)
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14 }
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15 %- maybe also 'usage' for other objects documented here.
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16 \arguments{
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17 \item{data}{ Tag/quality data: output of \code{read.eland.tags} or similar function }
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18 \item{srange}{ A range within which the binding peak separation is
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19 expected to fall. Should be larger than probe size to avoid artifacts. }
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20 \item{bin}{ Resolution (in basepairs) at which cross-corrrelation
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21 should be calculated. bin=1 is ideal, but takes longer to calculate. }
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22 \item{cluster}{ optional snow cluster for parallel processing }
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23 \item{debug}{ whether to print debug messages }
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24 \item{min.tag.count}{ minimal number of tags on the chromosome to be
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25 considered in the cross-correlation calculations }
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26 \item{acceptance.z.score}{ A Z-score used to determine if a given tag
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27 quality bin provides significant improvement to the strand cross-correlation }
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28 \item{remove.tag.anomalies}{ Whether to remove singular tag count peaks prior to
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29 calculation. This is recommended, since such positions may distort the
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30 cross-correlation profile and increase the necessary computational time. }
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31 \item{anomalies.z}{ Z-score for determining if the number of tags at a
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32 given position is significantly higher about background, and should be
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33 considered an anomaly.}
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34 \item{accept.all.tags}{ Whether tag alignment quality calculations
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35 should be skipped and all available tags should be accepted in the
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36 downstream analysis.}
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37 }
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38 \value{
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39 \item{cross.correlation }{ Cross-correlation profile as an $x/$y data.frame}
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40 \item{peak }{Position ($x) and height ($y) of automatically detected
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41 cross-correlation peak.}
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42 \item{whs} { Optimized window half-size for binding detection (based
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43 on the width of the cross-correlation peak) }
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44 \item{quality.bin.acceptance} { A list structure, describing the
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45 effect of inclusion of different tag quality bins on
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46 cross-correlation, and a resolution on which bins should be
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47 considered.
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48 \item{informative.bins} { A boolean vector indicating whether the
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49 inclusion of tags from the tag quality bin specified in the name
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50 attribute significantly increases cross-correlation profile near
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51 the peak.}
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52 \item{quality.cc} { A list giving the cross-correlation profile
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53 after the inclusion of the tags from different quality bins }
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54 }
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55 }
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