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