SCANVISmerge: merges multiple SCANVISsamples

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

Description

With this function, the RRS scores and number of supporting reads across a number of samples are collected into matrices by collecting the union of all SJs. Furthermore, a representative sample is assembled by computing the mean (or median) of RRSs and supporting reads across all samples - this may be used to visualize a cohort in one figure (see SCANVISvisual).

Usage

SCANVISmerge(scn, method = "mean", roi = NULL, gen = NULL)

Arguments

scn	list of SCANVISmatrices OR character vector of urls pointing to SCANVISmatrix outputs
method	method for computing a RRS/uniq.reads representative, either "mean" or "median" (default="mean")
roi	NULL for all SJs OR chromosome name for a query chromosome (eg. chr1) OR 3 bit vector (chr, start, end) indicating region of interest OR a vector with one or more gene names (default=NULL in which case all SJs are merged)
gen	gencode object as generated by SCANVISannotation which must be supplied if roi is a list of one or more gene names, otherwise NULL (default=NULL)

Value

Returns a list object ready for use in SCANVISvisual with the following details:

RRS	a matrix with RRS scores for each sample (columns) and the union of SJs across all samples (rows)
NR	a matrix with number of SJ reads each sample (columns) and the union of SJs across all samples (rows)
MUTS	a binary matrix with 1 indicating presence of a mutation (row) in a sample (column), generated only if samples submitted were variant-mapped SJs
SJ	a representative sample with mean/median RRS and uniq.reads that can be used in SCANVISvisual to visualize sample cohort
roi	genomic coordinates for region of interest used to derive resulting data

Note

For 50 or more samples, roi cannot be NULL as resulting matrices may be too large. For cohort agglomeration, please consider agglomerating chromosome by chromosome.

See Also

SCANVISscan, SCANVISlinkvar, SCANVISvisual

Examples

data(SCANVISexamples)
### merge all SJs across in sample list GBM
GBM.merged<-SCANVISmerge(GBM)
### only merge SJs intersecting with gene PTGDS
GBM.merged<-SCANVISmerge(GBM,'mean','PTGDS',gen19)

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