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6
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1 \name{get.broad.enrichment.clusters}
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2 \alias{get.broad.enrichment.clusters}
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3 %- Also NEED an '\alias' for EACH other topic documented here.
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4 \title{ Determine broad clusters of enrichment }
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5 \description{
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6 Scan chromosomes with a pre-defined window size, comparing scaled ChIP
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7 and input tag coutns to see if their ratio exceeds that expected from
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8 a Poisson process (normalized for dataset size).
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9 }
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10 \usage{
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11 get.broad.enrichment.clusters(chip.tags, input.tags, window.size=1e3,z.thr=3,tag.shift=146/2)
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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{chip.tags}{ foreground tag vector list }
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16 \item{input.tags}{ background tag vector list }
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17 \item{window.size}{ window size to be used for tag counting }
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18 \item{z.thr}{ Z-score to be used as a significance threshold }
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19 \item{tag.shift}{ number of base pairs by which positive and negative
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20 tag coordinates should be shifted towards eachother (half of binding
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21 peak separation distance)}
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22 }
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23 \value{
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24 A list of elements corresponding to chromosomes, with each element
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25 being an $s/$e/$rv data.frame giving the starting, ending positions and the log2
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26 enrichment estimate for that region.
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27 }
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