Description Usage Arguments Details Value Author(s) References Examples
Call peaks from a list of p-values corresponding to window-level
tests on a genomic partition of ChIP-seq counts. Used within the main peak
calling function, BQ
.
1 2 | call.peaks(window.pvals, method = c("BY", "BH", "none"), start, end,
chromosomes, alpha = 0.05)
|
window.pvals |
Vector of p-values, with each element corresponding to a
window of a genomic partition. Typically obtained from the
|
method |
Correction method applied to |
start |
Vector of the genomic start locations corresponding to the supplied p-values. |
end |
Vector of the genomic end locations corresponding to the supplied p-values. |
chromosomes |
Vector of the chromosome names corresponding to the supplied p-values. |
alpha |
The desired significance threshold in (0, 0.5). |
After correcting for multiple testing using the adjustment specified
by method
, windows that are significant according to the threshold
alpha
are merged if adjacent and retained as candidate regions.
Simes' procedure is used to combine the window-level p-values in each
candidate region into a region-level p-value. The Benjamini-Hochberg
procedure is applied to the resulting candidate regions and those that
exceed the significance threshold alpha
are returned as peaks.
The called peaks as a dataframe with variables:
start |
Genomic start locations of the called peaks. |
end |
Genomic end locations of the called peaks. |
width |
Width of the called peaks. |
chr |
Chromosomes of the called peaks. |
P.val |
p-values of the called peaks (aggregated from the windows comprising the peak using Simes' procedure). |
Q.val |
q-values of the called peaks (computing using the Benjamini-Hochberg procedure). |
Emily Goren (emily.goren@gmail.com).
Benjamini and Hochberg (1995) "Controlling the false discovery rate: a practical and powerful approach to multiple testing" Journal of the Royal Statistical Society Series B, 57: 289-300.
Benjamini and Yekutieli (2001) "The control of the false discovery rate in multiple testing under dependency" Annals of Statistics. 29: 1165-1188.
Simes (1986) "An improved Bonferroni procedure for multiple tests of significance" Biometrika, 73(3): 751-754.
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