makeVariantNames

variants


Create interpretable splice variant names
taking format GENE_EVENT_VARIANT/ORDER_TYPE.
GENE is based on geneName if available, and geneID otherwise.
EVENT and VARIANT enumerate events and variants for the same gene
and event, respectively. ORDER indicates the total number of
variants in the same event (e.g. 1/2 refers to the first out of two
splice variants in the event). TYPE is based on variantType.


internal

SGSeq is a software package for analyzing splice events from
RNA-seq data. Input data are sequence reads mapped to a reference
genome in BAM format. Genes are represented as a genome-wide
splice graph, which can be obtained from existing annotation or
can be predicted from the data. Splice events are identified
from the graph and are quantified locally using structurally
compatible reads at the start or end of each splice variant.
The package includes functions for splice event prediction,
quantification, visualization and interpretation.

makeVariantNames: Create interpretable splice variant names

Description

Usage

Arguments

Value

Examples