Description Usage Arguments Details Value Examples
Assess the consistency between ChIP-Seq replicates according to Qunhua Li et al.
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chipSamples |
vector of file names of immuno-precipitated samples in |
inputSamples |
vector of file names of control samples in |
org |
organism as described in the |
assembly |
assembly name: |
version |
assembly version: |
readLength |
length of reads (helps identify phantom peak), if |
shiftRange |
strand shifts at which cross-correlation is evaluated |
binSize |
step size for |
crossCorrelationPeakShift |
user-defined cross-correlation peak shift (when given, SPP does not try to detect the peak shift automatically) |
invalidCrossCorrelationPeaks |
strand shifts to exclude (to avoid phantom peaks) |
halfWidth |
a numerical value to truncate the peaks to; |
overlapRatio |
a value between 0 and 1. It controls how much overlaps two peaks need to have to be considered as calling the same region. It is the ratio of overlap / short peak of the two. When set to 0, two peaks are deemed as calling the same region, if they overlap by at least 1 bp |
isBroadPeak |
if broadpeak is used, set to |
cluster |
a |
Assess the consistency between ChIP-Seq replicates according to Qunhua Li et al.:
Ref: Qunhua Li, James B. Brown, Haiyan Huang, and Peter J. Bickel: Measuring reproducibility of high-throughput experiments. Ann Appl Stat. 2011 October 13
The irreproducible discovery rate (IDR) is a measure for the probability
that a peak is called in a ChIP-Seq sample, if it has been called in another
sample. Peaks that result from biological activity should be called
consistently between replicates. They are assigned a low IDR. In contrast,
peaks that are noise are typically not called in all replicates and are
assigned a high IDR.
The output of this function is meant to be used as input to the function
plotIDR
, which generates plots for the assessment of the IDR of
ChIP-Seq replicates. Refer to Qunhua Li et al (2011) for an explanation on
how to interpret the plots.
object that is suitable as input to plotIDR
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