estimateSizeFactors | R Documentation |
Given a table of raw read counts from ChIP-seq experiments,
estimateSizeFactors
returns estimated size factors representing
relative sequencing depths of the ChIP-seq samples.
estimateSizeFactors(counts, subset = NULL)
counts |
A matrix or data frame consisting of read counts. Each row represents an observation (typically a genomic interval) and each column a ChIP-seq sample. Objects of other types are coerced to a matrix. |
subset |
An optional vector specifying a subset of observations to be used in the estimation process. |
This function utilizes the median ratio strategy to deduce size factors (see "References" for details). It's primarily for being used by the MA normalization process to select an optimal baseline sample, and in most cases you don't need to call this function directly. It may help, however, when you want to specify the baseline sample by your own criterion.
estimateSizeFactors
returns a numeric vector specifying the
size factors.
Anders, S. and W. Huber, Differential expression analysis for sequence count data. Genome Biol, 2010. 11(10): p. R106.
normalize
for the MA normalization process.
data(H3K27Ac, package = "MAnorm2") attr(H3K27Ac, "metaInfo") # Use all the genomic intervals. estimateSizeFactors(H3K27Ac[4:8]) # Use only the genomic intervals occupied by all the ChIP-seq samples. estimateSizeFactors(H3K27Ac[4:8], subset = apply(H3K27Ac[9:13], 1, all))
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