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6
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1 \name{get.mser}
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2 \alias{get.mser}
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3 %- Also NEED an '\alias' for EACH other topic documented here.
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4 \title{ Calculate minimal saturated enrichment fold ratio }
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5 \description{
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6 Determine if the dataset has reached absolute saturation, or otherwise
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7 find minimal fold enrichment ratio above which the detection of peaks
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8 has stabilized enough to meet the saturation criteria.
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9 }
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10 \usage{
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11 get.mser(signal.data, control.data, n.chains = 5, step.size = 1e+05, chains = NULL, cluster = NULL, test.agreement = 0.99, return.chains = F, enrichment.background.scales = c(1), n.steps = 1, ...)
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12 }
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13 %- maybe also 'usage' for other objects documented here.
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14 \arguments{
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15 \item{signal.data}{ signal tag vector list }
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16 \item{control.data}{ control tag vector list }
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17 \item{n.chains}{ number of dataset subsamples to use }
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18 \item{step.size}{ subsampling step describing the saturation
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19 criteria. The criteria requires the set of detected binding sites to
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20 be stable (as described by the \code{test.agreement} param) when the
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21 number of tags in the dataset is reduced by \code{step.size}. The
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22 value can either be an integer above one, in which case it specifies a fixed
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23 number of tags, or a real value below one, in which case it
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24 specifies the fraction of tags that should be removed (e.g. 0.1 will
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25 remove 10% of tags).
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26 }
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27 \item{test.agreement}{ Fraction of the detected peaks that should
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28 agree between the full and subsampled datasets. }
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29 \item{chains}{ optional parameter, giving pre-calculated chains }
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30 \item{cluster}{ optional \code{snow} cluster to parallelize processing }
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31
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32 \item{return.chains}{ whether subsampled dataset results should be returned as
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33 well }
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34 \item{enrichment.background.scales}{ one or multiple window scales at
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35 which the background tag density should be assessed. See
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36 \code{enrichment.background.scales} in
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37 \code{\link{find.binding.positions}}. If multiple scales are provided,
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38 multiple MSER estimates will be returned.}
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39 \item{\dots}{ additional parameters should be the same as those passed
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40 to the \code{\link{find.binding.positions}}}
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41 }
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42 \value{
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43 A single, or multple (if multiple \code{enrichment.background.scales} were
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44 provided) MSER value. A value of 1 or very close to it implies that
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45 the dataset has reached absolute saturation based on the given criteria.
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46 }
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