pausingIndex {groHMM} | R Documentation |
Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, use the argument 'mc.cores'.
pausingIndex(features, reads, size = 50, up = 1000, down = 1000, UnMAQ = NULL, debug = FALSE, ...)
features |
A GRanges object representing a set of genomic coordinates. |
reads |
A GRanges object representing a set of mapped reads. |
size |
The size of the moving window. |
up |
Distance upstream of each f to align and histogram. |
down |
Distance downstream of each f to align and histogram (NULL). |
UnMAQ |
Data structure representing the coordinates of all un-mappable regions in the genome. |
debug |
If set to TRUE, provides additional print options. Default: FALSE |
... |
Extra argument passed to mclapply |
Returns a data.frame of the pausing indices for the input genes.
Returns the pausing index for different genes.
Charles G. Danko and Minho Chae.
features <- GRanges("chr7", IRanges(2394474,2420377), strand="+") reads <- as(readGAlignments(system.file("extdata", "S0mR1.bam", package="groHMM")), "GRanges") ## Not run: # pi <- pausingIndex(features, reads)