callpeak {CSSP} | R Documentation |
Call enriched bins based on the CSSP model.
callpeak(fit, chip, fold = 1.8, min.count = 0, qval = 0.05, method = "", depth = fit@lambday) ## S4 method for signature 'CSSPFit' callpeak(fit, chip, fold = 1.8, min.count = 0, qval = 0.05, method = "", depth = fit@lambday)
fit |
A CSSPFit-class object containing the fitted CSSP model. |
chip |
A numeric vector containing the bin counts for the ChIP sample. |
fold |
A numeric value for the fold change threshold for peak calling. |
min.count |
A numeric value for the minimum ChIP count threshold for peak calling. |
qval |
A numeric value for the false-discovery rate to be controlled. Default: 0.05. |
method |
A character value. By default, "min.count" is used to threshold the ChIP bin counts. If 'method=="post"', "min.count" is used to threshold the posterior bin-level poisson intensities. |
depth |
A numeric value for the sequencing depth corresponding to the ChIP sample of the "chip" argument. If not provided, sequencing depth of "fit" is used. |
A numeric vector of locations for binding bins.
Chandler Zuo zuo@stat.wisc.edu
data( sampleFit ) data( bin.data ) callpeak( sampleFit, chip = bin.data@tagCount, fold = 1, min.count = 0 )