slots: Accessing and replacing metadata columns

Description

Accessor and replacement functions for metadata columns.

Usage

type(x) <- value
txName(x)
txName(x) <- value
geneName(x)
geneName(x) <- value
featureID(x)
featureID(x) <- value
geneID(x)
geneID(x) <- value
splice5p(x)
splice5p(x) <- value
splice3p(x)
splice3p(x) <- value
from(x) <- value
to(x) <- value
segmentID(x)
segmentID(x) <- value
variantID(x)
variantID(x) <- value
eventID(x)
eventID(x) <- value
closed5p(x)
closed5p(x) <- value
closed3p(x)
closed3p(x) <- value
closed5pEvent(x)
closed5pEvent(x) <- value
closed3pEvent(x)
closed3pEvent(x) <- value
variantType(x)
variantType(x) <- value
variantName(x)
variantName(x) <- value
featureID5p(x)
featureID5p(x) <- value
featureID3p(x)
featureID3p(x) <- value
featureID5pEvent(x)
featureID5pEvent(x) <- value
featureID3pEvent(x)
featureID3pEvent(x) <- value
## S3 method for class 'Features':
type(x)
## S3 method for class 'Paths':
type(x)
## S3 method for class 'Counts':
type(x)
## S3 method for class 'Features':
type(x) <- value
## S3 method for class 'Paths':
type(x) <- value
## S3 method for class 'Counts':
type(x) <- value
## S3 method for class 'Features':
txName(x)
## S3 method for class 'Paths':
txName(x)
## S3 method for class 'Counts':
txName(x)
## S3 method for class 'Features':
txName(x) <- value
## S3 method for class 'Paths':
txName(x) <- value
## S3 method for class 'Counts':
txName(x) <- value
## S3 method for class 'Features':
geneName(x)
## S3 method for class 'Paths':
geneName(x)
## S3 method for class 'Counts':
geneName(x)
## S3 method for class 'Features':
geneName(x) <- value
## S3 method for class 'Paths':
geneName(x) <- value
## S3 method for class 'Counts':
geneName(x) <- value
## S3 method for class 'SGFeatures':
featureID(x)
## S3 method for class 'Paths':
featureID(x)
## S3 method for class 'Counts':
featureID(x)
## S3 method for class 'SGFeatures':
featureID(x) <- value
## S3 method for class 'Paths':
featureID(x) <- value
## S3 method for class 'Counts':
featureID(x) <- value
## S3 method for class 'SGFeatures':
geneID(x)
## S3 method for class 'Paths':
geneID(x)
## S3 method for class 'Counts':
geneID(x)
## S3 method for class 'SGFeatures':
geneID(x) <- value
## S3 method for class 'Paths':
geneID(x) <- value
## S3 method for class 'Counts':
geneID(x) <- value
## S3 method for class 'SGFeatures':
splice5p(x)
## S3 method for class 'SGSegments':
splice5p(x)
## S3 method for class 'SGFeatureCounts':
splice5p(x)
## S3 method for class 'SGFeatures':
splice5p(x) <- value
## S3 method for class 'SGSegments':
splice5p(x) <- value
## S3 method for class 'SGFeatureCounts':
splice5p(x) <- value
## S3 method for class 'SGFeatures':
splice3p(x)
## S3 method for class 'SGSegments':
splice3p(x)
## S3 method for class 'SGFeatureCounts':
splice3p(x)
## S3 method for class 'SGFeatures':
splice3p(x) <- value
## S3 method for class 'SGSegments':
splice3p(x) <- value
## S3 method for class 'SGFeatureCounts':
splice3p(x) <- value
## S3 method for class 'Paths':
segmentID(x)
## S3 method for class 'SGVariantCounts':
segmentID(x)
## S3 method for class 'Paths':
segmentID(x) <- value
## S3 method for class 'SGVariantCounts':
segmentID(x) <- value
## S3 method for class 'Paths':
from(x)
## S3 method for class 'SGVariantCounts':
from(x)
## S3 method for class 'Paths':
from(x) <- value
## S3 method for class 'SGVariantCounts':
from(x) <- value
## S3 method for class 'Paths':
to(x)
## S3 method for class 'SGVariantCounts':
to(x)
## S3 method for class 'Paths':
to(x) <- value
## S3 method for class 'SGVariantCounts':
to(x) <- value
## S3 method for class 'SGVariants':
eventID(x)
## S3 method for class 'SGVariantCounts':
eventID(x)
## S3 method for class 'SGVariants':
eventID(x) <- value
## S3 method for class 'SGVariantCounts':
eventID(x) <- value
## S3 method for class 'SGVariants':
variantID(x)
## S3 method for class 'SGVariantCounts':
variantID(x)
## S3 method for class 'SGVariants':
variantID(x) <- value
## S3 method for class 'SGVariantCounts':
variantID(x) <- value
## S3 method for class 'SGVariants':
closed5p(x)
## S3 method for class 'SGVariantCounts':
closed5p(x)
## S3 method for class 'SGVariants':
closed5p(x) <- value
## S3 method for class 'SGVariantCounts':
closed5p(x) <- value
## S3 method for class 'SGVariants':
closed3p(x)
## S3 method for class 'SGVariantCounts':
closed3p(x)
## S3 method for class 'SGVariants':
closed3p(x) <- value
## S3 method for class 'SGVariantCounts':
closed3p(x) <- value
## S3 method for class 'SGVariants':
closed5pEvent(x)
## S3 method for class 'SGVariantCounts':
closed5pEvent(x)
## S3 method for class 'SGVariants':
closed5pEvent(x) <- value
## S3 method for class 'SGVariantCounts':
closed5pEvent(x) <- value
## S3 method for class 'SGVariants':
closed3pEvent(x)
## S3 method for class 'SGVariantCounts':
closed3pEvent(x)
## S3 method for class 'SGVariants':
closed3pEvent(x) <- value
## S3 method for class 'SGVariantCounts':
closed3pEvent(x) <- value
## S3 method for class 'SGVariants':
variantName(x)
## S3 method for class 'SGVariantCounts':
variantName(x)
## S3 method for class 'SGVariants':
variantName(x) <- value
## S3 method for class 'SGVariantCounts':
variantName(x) <- value
## S3 method for class 'SGVariants':
variantType(x)
## S3 method for class 'SGVariantCounts':
variantType(x)
## S3 method for class 'SGVariants':
variantType(x) <- value
## S3 method for class 'SGVariantCounts':
variantType(x) <- value
## S3 method for class 'SGVariants':
featureID5p(x)
## S3 method for class 'SGVariantCounts':
featureID5p(x)
## S3 method for class 'SGVariants':
featureID5p(x) <- value
## S3 method for class 'SGVariantCounts':
featureID5p(x) <- value
## S3 method for class 'SGVariants':
featureID3p(x)
## S3 method for class 'SGVariantCounts':
featureID3p(x)
## S3 method for class 'SGVariants':
featureID3p(x) <- value
## S3 method for class 'SGVariantCounts':
featureID3p(x) <- value
## S3 method for class 'SGVariants':
featureID5pEvent(x)
## S3 method for class 'SGVariantCounts':
featureID5pEvent(x)
## S3 method for class 'SGVariants':
featureID5pEvent(x) <- value
## S3 method for class 'SGVariantCounts':
featureID5pEvent(x) <- value
## S3 method for class 'SGVariants':
featureID3pEvent(x)
## S3 method for class 'SGVariantCounts':
featureID3pEvent(x)
## S3 method for class 'SGVariants':
featureID3pEvent(x) <- value
## S3 method for class 'SGVariantCounts':
featureID3pEvent(x) <- value

Arguments

Object containing metadata column

value

Replacement value

Value

Content of metadata column for accessor functions or updated object for replacement functions.

Details

S4 classes defined in the SGSeq package contain metadata columns that store information for each element in the object. For example, class TxFeatures contains a column type that indicates feature type. The specific columns contained in an object depend on its class.

Examples

Run this code

head(type(txf_ann))
head(type(sgf_ann))

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