estimateFDR {wavClusteR} | R Documentation

## Estimate False Discovery Rate within the relative substitution frequency support by integrating PAR-CLIP data and RNA-Seq data

### Description

Estimate upper and lower bounds for the False Discovery Rate within the relative substitution frequency (RSF) support by integrating PAR-CLIP data and RNA-Seq data (current version makes use of unstranded RNA-Seq)

### Usage

    estimateFDR(countTable, RNASeq, substitution = 'TC', minCov = 20,
    span = 0.1, cores = 1, plot = TRUE, verbose = TRUE, ...)

### Arguments

`countTable` | A GRanges object, corresponding to a count table as returned by the getAllSub function
`RNASeq` | GRanges object containing aligned RNA-Seq reads as returned by readSortedBam
`substitution` | A character indicating which substitution is induced by the experimental procedure (e.g. 4-SU treatment - a standard in PAR-CLIP experiments - induces T to C transitions and hence substitution = 'TC' in this case.)
`minCov` | An integer defining the minimum coverage required at a genomic position exhibiting a substitution. Genomic positions of coverage less than `minCov` are discarded. Default is 20 (see Details).
`span` | A numeric indicating the width of RSF intervals to be considered for FDR computation. Defauls is 0.1 (i.e. 10 intervals are considered spanning the RSF support (0,1]
`cores` | An integer defining the number of cores to be used for parallel processing, if available. Default is 1.
`plot` | Logical, if TRUE a dotchart with cluster annotations is produced
`verbose` | Logical, if TRUE processing steps are printed
`...` | Additional parameters to be passed to the `plot` function

### Details

For details on the FDR computation, please see Comoglio, Sievers and Paro.

### Value

A list with three slots, containing upper and lower FDR bounds, and the total number of positive instances each RSF interval. If `plot`, these three vectors are depicted as a line plot.

### Note

The approach used to compute the upper bound for the FDR is very conservative. See supplementary information in Comoglio et al. for details.

### Author(s)

Federico Comoglio and Cem Sievers

### See Also

`readSortedBam`, `getAllSub` Comoglio F, Sievers C and Paro R (2015) Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data, BMC Bioinformatics 16, 32.

[Package wavClusteR version 2.12.1 Index]