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1 \name{get.smoothed.enrichment.mle}
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2 \alias{get.smoothed.enrichment.mle}
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3 %- Also NEED an '\alias' for EACH other topic documented here.
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4 \title{ Calculate chromosome-wide profiles of smoothed enrichment estimate }
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5 \description{
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6 Given signal and control tag positions, the method calculates log2
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7 signal to control enrichment esimates (maximum likelihood) for each
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8 chromosome, based on the smoothed tag density profile (see \link{get.smoothed.tag.density}).
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9 }
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10 \usage{
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11 get.smoothed.enrichment.mle(signal.tags, control.tags, bandwidth = 150,tag.shift = 146/2, step = 50)
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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.tags}{ signal chromosome tag coordinate vectors (e.g. output
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16 of \code{\link{select.informative.tags}} }
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17 \item{control.tags}{ control (input) tags }
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18 \item{pseudocount}{ pseudocount value to be added to tag density -
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19 defaults to 1 }
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20 other parameters (such as bandwidth, step.size and tag.shift) are
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21 passed to \link{get.smoothed.tag.density} - see appropriate reference
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22 for details.
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23 }
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24 \value{
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25 A list of elements corresponding to chromosomes, with each element
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26 being an $x/$y data.frame giving the position and associated
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27 log2 signal/control enrichment estimate.
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28 }
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29 \seealso{ \code{\link{writewig}} }
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30 \examples{
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31 # get smoothed enrichment estimate profile using 500bp bandwidth at
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32 # 50bp steps
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33 smoothed.M <- get.smoothed.enrichment.mle(chip.data,bandwidth=500,step=50);
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34 writewig(smoothed.M,"example.smoothedM.wig","Example smoothed log2 intensity ratio estimate");
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35 } |
