regionSummary: regionSummary

In AllelicImbalance: Investigates Allele Specific Expression

Description

Gives a summary of AI-consistency for a transcript

Usage

regionSummary(x, ...)

## S4 method for signature 'ASEset'
regionSummary(x, region, strand = "*", return.class = "RegionSummary", ...)

Arguments

x	ASEset object
...	arguments to forward to internal functions
region	to summmarize over, the object can be a GRanges, GRangesList
strand	can be "+", "-" or "*"
return.class	"array" or "list".

Details

From a given set of e.g. transcripts exon ranges the function will return a summary for the sum of all exons. Phase information, reference and alternative allele is required.

A limitation comes to the strand-specificness. At the moment it is not possible to call over more than one strand type using the strands in region. This will be improved before going to release.

to calculate the direction and binomial p-values of AI the mapbias stored in the ASEset is used. see '?mapBias'.

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples

data(ASEset)
a <- ASEset
# Add phase
set.seed(1)
p1 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
p2 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
p <- matrix(paste(p1,sample(c("|","|","/"), size=nrow(a)*ncol(a), replace=TRUE), p2, sep=""),
	nrow=nrow(a), ncol(a))

phase(a) <- p

#add alternative allele information
mcols(a)[["alt"]] <- inferAltAllele(a)

# in this example each and all snps in the ASEset defines the region
region <- granges(a)
t <- regionSummary(a, region)

# in this example two overlapping subsets of snps in the ASEset defines the region
region <- split(granges(a)[c(1,2,2,3)],c(1,1,2,2))
t <- regionSummary(a, region)

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.