estimateSeqDepth-methods {exomePeak2} | R Documentation |
estimateSeqDepth
estimate sequencing depth size factors for each MeRIP-seq samples used in peak statistics quantification.
Under default setting, the sequencing depth are estimated by the robust estimator defined in package DESeq
.
i.e. the median of the ratios to the geometric means of peak counts.
estimateSeqDepth(sep, from = c("Background", "Modification", "All"), ...) ## S4 method for signature 'SummarizedExomePeak' estimateSeqDepth(sep, from = c("Background", "Modification", "All"), ...)
sep |
a |
from |
a
Under the default settings, the sequencing depth size factors are estimated from the background control regions. |
... |
inherited from |
The function takes the input of a SummarizedExomePeak
object,
and it estimates the sequencing depth size factors by the columns of its assay.
This function will return a SummarizedExomePeak
object containing newly estimated sequencing depth size factors.
### Load the example SummarizedExomPeak object f1 = system.file("extdata", "sep_ex_mod.rds", package="exomePeak2") sep <- readRDS(f1) ### Estimate the sequencing depth size factors sep <- estimateSeqDepth(sep) sep$sizeFactor