SCANVISscan: SCore and ANnotate splice junctions

In nygenome/SCANVIS: SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

Description

This function annotates and scores splice junctions (SJs) supplied in bed format (coordinates plus read support) and gene annotations (see SCANVISannotation). Each SJ will get annotated by gene name and junction type, with unannotated SJs (USJs) falling into one of the following groups: exon.skip, alt3p, alt5p, IsoSwitch, Unknown and NE (Novel Exons) - see below. USJs are also checked and marked for in or out of frame shifts. Each SJ is scored by a Relative Read Support (RRS) score defined as the ratio of the junction read supportto the median read support of annotated SJs within a RRS genomic region, that being defined as the minimum interval that contains at least one gene overlapping the SJ and at least one annotated SJ overlapping the gene/s wtihin the interval. Novel Exons (NEs) are defined by USJ pairs that coincide in annotated intronic regions and are scored by the mean RRS of the supporting USJs and by a Relative Read Coverage (RRC) score when the bam file is supplied.

Usage

SCANVISscan(sj, gen, Rcut = 5, bam = NULL, samtools = NULL)

Arguments

sj	SJ matrix with colnames chr,start,end,uniq.reads
gen	gencode object as generated by SCANVISannotation
Rcut	min read cutoff; only SJs with >=Rcut reads are retained (Default=5)
bam	url to bam file for NE RRC computation (default=NULL)
samtools	url to samtools function, MUST be specified if bam is supplied (default=NULL)

Value

An extension of the input SJ matrix for relevant SJs, with additional rows for NE junction pairs, as well as the following additional columns:

JuncType	describes junction type as annot for annotated SJs and one of the following for unannotated SJs: exon.skip, alt3p, alt5p, IsoSwitch, Unknown and NE (Novel Exons) where exon.skip refers to SJs that skip an exon present in all isoforms, alt3p refers to an alternative 3 prime acceptor site, alt5p refers to an alternative 5 prime donor sites, IsoSwitch refers to SJs aligning to mutually exclusive isoforms such that a novel unannotated isoform is incurred, Unknown SJs have coordinates that do not align to any exons and NE (Novel Exons) refers to SJ pairs with the start of one SJ and the end coordinate of the other SJ coinciding in an intronic region
gene_name	genes that intersect with the SJ (multiple genes are comma separated
RRS	Relative Read Support score defined as x/(x+y) where x is the query junction read support and y is the median read support of annotated SJs in the RRS genomic_interval
genomic_interval	interval used for the RRS computation
FrameStatus	frame shifts induced by unannotated SJs, where INframe indicates no frame-shift in any gene isoforms, OUTframe indicates frame-shifting in ALL gene isoforms and all other entries indicating frame shifts for specified isoforms. FrameStatus is marked NA for annotated SJs)
RRC	Relative Read Coverage score generated for NEs only, and computed only if the bam file is supplied

See Also

SCANVISannotation, SCANVISlinkvar, SCANVISvisual

Examples

data(SCANVISexamples)
head(gbm3) #required SJ format
gbm3.scn<-SCANVISscan(sj=gbm3,gen=gen19,Rcut=5)
head(gbm3.scn)
### to compute RRC scores for NEs, run as follows:
#gbm3.scn<-SCANVISscan(gbm3,gen19,5,bam=<BAM>,samtools=<SAMTOOLS>)

nygenome/SCANVIS documentation built on July 19, 2019, 4:57 a.m.