biovizBase (version 1.20.0)

isMatchedWithModel: Utils for Splicing Summary

Description

Utilities used for summarizing isoforms

Usage

isJunctionRead(cigar)
isMatchedWithModel(model, gr)

Arguments

cigar

A CIGAR string vector.

model

A GRanges object.

gr

A GRanges object.

Value

Logical vectors.

Details

isJunctionRead simply parsing the CIGAR string to see if there is "N" in between and return a logical vector of the same length as cigar parameters, indicate it's junction read or not.

isMatchedWithModel mapping gr to model, and counting overlapped cases for each row of model, If gr contains all the read, this will return a logical vector of the same length as gr, and indicate if each read is the support for this model. NOTICE: we only assume it's a full model, so each model here is simply one isoform. So we only treat the gaped reads which only overlapped with two consecutive exons in model as one support for it.

Examples

library(GenomicAlignments)
bamfile <- system.file("extdata", "SRR027894subRBM17.bam",
  package="biovizBase")
## get index of junction read
which(isJunctionRead(cigar(readGAlignments(bamfile))))
##
model <- GRanges("chr1", IRanges(c(10, 20, 30, 40), width  = 5))
gr <- GRanges("chr1", IRanges(c(10, 10, 12, 22, 33), c(31, 40, 22, 32,
  44)))
isMatchedWithModel(model, gr)