getDistrs: Compute fragment start and fragment length distributions
In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description Usage Arguments Value Author(s) Examples

Compute fragment start distributions by using reads aligned to genes with only one annotated variant. Estimate fragment length distribution using fragments aligned to long exons (>1000nt). Fragment length is defined as the distance between the start of the left-end read and the end of the right-end read.

1 2	getDistrs(DB, bam, pbam, islandid=NULL, verbose=FALSE, nreads=4*10^6, readLength, min.gt.freq = NULL, tgroups=5, mc.cores=1)

`DB`	Annotated genome. Object of class `knownGenome` as returned by `procGenome`.
`bam`	Aligned reads, as returned by `scanBam`. It must be a list with elements 'qname', 'rname', 'pos' and 'mpos'. Ignored when argument `pbam` is specified.
`pbam`	Processed BAM object of class `procBam`, as returned by function `procBam`. Arguments `bam` and `readLength` are ignored when `pbam` is specified.
`islandid`	Island IDs of islands to be used in the read start distribution calculations (defaults to genes with only one annotated variant)
`verbose`	Set to `TRUE` to print progress information.
`nreads`	To speed up computations, only the first `nreads` are used to obtain the estimates. The default value of 4 milions usually gives highly precise estimates.
`readLength`	Read length in bp, e.g. in a paired-end experiment where 75bp are sequenced on each end one would set `readLength=75`.
`min.gt.freq`	The target distributions cannot be estimated with precision for gene types that are very unfrequent. Gene types with relative frequency below `min.gt.freq` are merged, e.g. `min.gt.freq=0.05` means gene types making up for 5% of the genes in DB will be combined and a single read start and length distribution will be estimated for all of them.
`tgroups`	As an alternative to `min.gt.freq` you may specify the maximum number of distinct gene types to consider. A separate estimate will be obtained for the `tgroups` with highest frequency, all others will be combined.
`mc.cores`	Number of cores to use for parallel processing

An object of class readDistrs with slots:

`lenDis`	Table with number of fragments with a given length
`stDis`	Cumulative distribution function (object of type closure) for relative start position

Camille Stephan-Otto Attolini, David Rossell

data(K562.r1l1)
data(hg19DB)
bam0 <- rmShortInserts(K562.r1l1, isizeMin=100)

distrs <- getDistrs(hg19DB,bam=bam0,readLength=75)

#Fragment length distribution
plot(distrs,'fragLength')

#Fragment start distribution (relative to transcript length)
plot(distrs,'readSt')