SGVariants: Splice graph variants
In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description Usage Arguments Details Value Author(s) Examples

Creates an instance of S4 class SGVariants for storing splice variants.

1	SGVariants(x)

`x`	`GRangesList` of `SGFeatures` with appropriate outer metadata columns

SGVariants includes columns as described below.

from and to indicate the variant start and end, respectively. from nodes are splice donors (“D”) or transcript starts (“S”). to nodes are splice acceptors (“A”) or transcript ends (“E”).
type and featureID describe the variant in terms of the splice graph features that make up the variant.
segmentID specifies unique identifiers labelling unbranched segments of the splice graph.
closed5p indicates whether nodes in the variant can be reached from nodes outside of the variant exclusively through the from node.
closed3p indicates whether nodes in the variant can reach nodes outside of the variant exclusively through the to node.
closed5pEvent indicates whether nodes in the event can be reached from nodes outside of the event exclusively through the from node.
closed3pEvent indicates whether nodes in the event can reach nodes outside of the event exclusively through the to node.
geneID has the same interpretation as for SGFeatures.
eventID and variantID are unique identifiers for each event and variant, respectively.
featureID5p and featureID3p indicate representative features used for variant quantification at the start and end of the variant, respectively.
featureID5pEvent and featureID3pEvent indicate the ensemble of representative features at the start and end of the event, respectively.
txName indicates structurally compatible transcripts.
geneName behaves as for SGFeatures.
variantType indicates whether a splice variant is consistent with a canonical splice event (for a list of possible values, see the manual page for annotateSGVariants).
variantName provides a unique name for each splice variant (for details, see the manual page for makeVariantNames).