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pausingIndex(features, reads, size = 50, up = 1000, down = 1000, UnMAQ = NULL, debug = FALSE, ...)
features <- GRanges("chr7", IRanges(2394474,2420377), strand="+")
reads <- as(readGAlignments(system.file("extdata", "S0mR1.bam",
package="groHMM")), "GRanges")
## Not run:
# pi <- pausingIndex(features, reads)
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