SGVariants for storing
splice variants.
SGVariants(x)GRangesList of SGFeatures with appropriate
outer metadata columnsSGVariants object
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).