Align peaks in a ChIP-Seq experiment by removing the shift between reads aligned to the plus and the minus strands.
alignPeaks(x, strand, npeaks = 1000, bandwidth = 150, mc.cores=1)
Strand that each read was aligned to.
Number of peaks to be used to estimate the shift size.
Only reads with distance less than
Number of cores to be used for parallel computing
(passed on to
The procedure detects the
npeaks highest peaks (using reads
from both strands simultaneously).
Then it selects reads which are less than
bandwidth base pairs away from
any of the peaks.
Then it computes (a) the average distance between reads on the plus
strand and the closest peak, (b) the same distance for reads on the
minus strand. The mean difference between (a) and (b) is the estimated
Reads on the plus strand are shifted to the right, whereas reads on
the minus strands are shifted to the left.
CompressedIRangesList object with all reads shifted so that
the strand specific bias is no longer present.
signature(x = "IRangesList", strand = "list")
x corresponds to a chromosome, and each range gives
the start/end of a sequence.
strand indicates the strand for
the ranges in
signature(x = "RangedData", strand = "character")
x gives read start and end positions, and
the name of the variable in
values(x) containing the strand information.
signature(x = "list", strand = "character")
The method for
RangedData is applied to each element in
x separately, as each element may
have a different strand-specific bias.
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