normalizeChIPtoInput(input, response, dispersion=0.01, niter=6, loss="p", plot=FALSE,
verbose=FALSE, ...)
calcNormOffsetsforChIP(input, response, dispersion=0.01, niter=6, loss="p", plot=FALSE,
verbose=FALSE, ...)
"p"
for cumulative probabilities or "z"
for z-value.TRUE
, a plot of the fit is produced.TRUE
, working estimates from each iteration are output.plot
function.normalizeChIPtoInput
returns a list with componentscalcNormOffsetsforChIP
returns a numeric matrix of offsets.normalizeChIPtoInput
identifies significant enrichment for a ChIP-Seq mark relative to input values.
The ChIP-Seq mark might be for example transcriptional factor binding or an epigenetic mark.
The function works on the data from one sample.
Replicate libraries are not explicitly accounted for, and would normally be pooled before using this function.ChIP-Seq counts are assumed to be summarized by gene or similar genomic feature of interest.
This function makes the assumption that a non-negligible proportion of the genes, say 25% or more, are not truly marked by the ChIP-Seq feature of interest. Unmarked genes are further assumed to have counts at a background level proportional to the input. The function aligns the counts to the input so that the counts for the unmarked genes behave like a random sample. The function estimates the proportion of marked genes, and removes marked genes from the fitting process. For this purpose, marked genes are those with a Holm-adjusted mid-p-value less than 0.5.
The read counts are treated as negative binomial. The dispersion parameter is not estimated from the data; instead a reasonable value is assumed to be given.
calcNormOffsetsforChIP
returns a numeric matrix of offsets, ready for linear modelling.