Description Usage Arguments Details Value Examples
Determine the minimal saturated enrichment ratio (MSER) and the predicted sequencing depth (PSD).
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chip.data |
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input.data |
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binding.characteristics |
The binding characteristics calculated with |
step.size |
The amount of tags to add in every step to reach the saturation criteria. |
test.agreement |
Saturation criteria consistency in the set of binding positions when adding |
n.chains |
The number of subsampled chains. |
n.steps |
The number of steps to convergence. |
fold.enrichment |
The target fold enrichment. |
fdr |
FDR cutoff. |
cluster |
A snow cluster: |
Determine the minimal saturated enrichment ratio (MSER). The saturation criteria here is 99% consistency in the set of binding positions when adding 10,000 tags.
Determine the predicted sequencing depth.
A vector containing the minimal saturated enrichment ratio (MSER) and the predicted sequencing depth (PSD) in million tags.
1 2 3 4 | # call SPP to get the binding characteristics
bc <- calculateBindingCharacteristics("IP.bam", "input.bam", read.len=51)
# calculate MSER and PSD
minser <- mser(bc$chip.data, bc$input.data, bc$bc)
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