Description Usage Arguments Details Value Author(s) Examples

View source: R/spliceSummary-method.R

Utilities used for summarizing isoforms

1 2 | ```
isJunctionRead(cigar)
isMatchedWithModel(model, gr)
``` |

`cigar` |
A CIGAR string vector. |

`model` |
A GRanges object. |

`gr` |
A GRanges object. |

`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.

Logical vectors.

Tengfei Yin

1 2 3 4 5 6 7 8 9 10 | ```
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)
``` |

Bioconductor-mirror/biovizBase documentation built on June 1, 2017, 5:21 a.m.

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