mser: Assess saturation properties

In imbforge/encodeChIPqc: A set of useful ChIPseq QC metrics from the ENCODE project

Description

Determine the minimal saturated enrichment ratio (MSER) and the predicted sequencing depth (PSD).

Usage

mser(chip.data, input.data, binding.characteristics, step.size = 1e+05,
  test.agreement = 0.99, n.chains = 8, n.steps = 6, fold.enrichment = 2,
  fdr = 0.01, cluster = NULL)

Arguments

chip.data	spp tags of the ChIP sample calculated with calculateBindingCharacteristics.
input.data	spp tags of the input sample calculated calculateBindingCharacteristics.
binding.characteristics	The binding characteristics calculated with calculateBindingCharacteristics.
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 step.size tags.
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: cluster <- snow::makeCluster(cores).

Details

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.

Value

A vector containing the minimal saturated enrichment ratio (MSER) and the predicted sequencing depth (PSD) in million tags.

Examples

# 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)

imbforge/encodeChIPqc documentation built on May 18, 2019, 4:45 a.m.