estimateSeqDepth-methods: Method estimateSeqDepth

In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

Description

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.

Usage

estimateSeqDepth(sep, from = c("Background", "Modification", "All"), ...)

## S4 method for signature 'SummarizedExomePeak'
estimateSeqDepth(sep, from = c("Background", "Modification", "All"), ...)

Arguments

sep	a SummarizedExomePeak object.
from	a character specify the subset of features for sequencing depth estimation, can be one of c("Background", "Modification", "All"). Background The sequencing depths are estimated from the background control regions. This method could make the IP/input LFC estimates become closer to the true modification proportion. Modification The sequencing depths are estimated from the modification peaks/sites. All The sequencing depths are estimated from both the background and the modification regions. Under the default settings, the sequencing depth size factors are estimated from the background control regions.
...	inherited from estimateSizeFactorsForMatrix.

Details

The function takes the input of a SummarizedExomePeak object, and it estimates the sequencing depth size factors by the columns of its assay.

Value

This function will return a SummarizedExomePeak object containing newly estimated sequencing depth size factors.

See Also

normalizeGC

Examples

### 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

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.