SGSeq
Splice event prediction and quantification from RNA-seq data

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slots: Accessing and replacing metadata columns

slots: Accessing and replacing metadata columns
In SGSeq: Splice event prediction and quantification from RNA-seq data

Description Usage Arguments Details Value Author(s) Examples

Description

Accessor and replacement functions for metadata columns.

Usage

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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

## S4 method for signature 'Features'
type(x)

## S4 method for signature 'Paths'
type(x)

## S4 method for signature 'Counts'
type(x)

## S4 replacement method for signature 'Features'
type(x) <- value

## S4 replacement method for signature 'Paths'
type(x) <- value

## S4 replacement method for signature 'Counts'
type(x) <- value

## S4 method for signature 'Features'
txName(x)

## S4 method for signature 'Paths'
txName(x)

## S4 method for signature 'Counts'
txName(x)

## S4 replacement method for signature 'Features'
txName(x) <- value

## S4 replacement method for signature 'Paths'
txName(x) <- value

## S4 replacement method for signature 'Counts'
txName(x) <- value

## S4 method for signature 'Features'
geneName(x)

## S4 method for signature 'Paths'
geneName(x)

## S4 method for signature 'Counts'
geneName(x)

## S4 replacement method for signature 'Features'
geneName(x) <- value

## S4 replacement method for signature 'Paths'
geneName(x) <- value

## S4 replacement method for signature 'Counts'
geneName(x) <- value

## S4 method for signature 'SGFeatures'
featureID(x)

## S4 method for signature 'Paths'
featureID(x)

## S4 method for signature 'Counts'
featureID(x)

## S4 replacement method for signature 'SGFeatures'
featureID(x) <- value

## S4 replacement method for signature 'Paths'
featureID(x) <- value

## S4 replacement method for signature 'Counts'
featureID(x) <- value

## S4 method for signature 'SGFeatures'
geneID(x)

## S4 method for signature 'Paths'
geneID(x)

## S4 method for signature 'Counts'
geneID(x)

## S4 replacement method for signature 'SGFeatures'
geneID(x) <- value

## S4 replacement method for signature 'Paths'
geneID(x) <- value

## S4 replacement method for signature 'Counts'
geneID(x) <- value

## S4 method for signature 'SGFeatures'
splice5p(x)

## S4 method for signature 'SGSegments'
splice5p(x)

## S4 method for signature 'SGFeatureCounts'
splice5p(x)

## S4 replacement method for signature 'SGFeatures'
splice5p(x) <- value

## S4 replacement method for signature 'SGSegments'
splice5p(x) <- value

## S4 replacement method for signature 'SGFeatureCounts'
splice5p(x) <- value

## S4 method for signature 'SGFeatures'
splice3p(x)

## S4 method for signature 'SGSegments'
splice3p(x)

## S4 method for signature 'SGFeatureCounts'
splice3p(x)

## S4 replacement method for signature 'SGFeatures'
splice3p(x) <- value

## S4 replacement method for signature 'SGSegments'
splice3p(x) <- value

## S4 replacement method for signature 'SGFeatureCounts'
splice3p(x) <- value

## S4 method for signature 'Paths'
segmentID(x)

## S4 method for signature 'SGVariantCounts'
segmentID(x)

## S4 replacement method for signature 'Paths'
segmentID(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
segmentID(x) <- value

## S4 method for signature 'Paths'
from(x)

## S4 method for signature 'SGVariantCounts'
from(x)

## S4 replacement method for signature 'Paths'
from(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
from(x) <- value

## S4 method for signature 'Paths'
to(x)

## S4 method for signature 'SGVariantCounts'
to(x)

## S4 replacement method for signature 'Paths'
to(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
to(x) <- value

## S4 method for signature 'SGVariants'
eventID(x)

## S4 method for signature 'SGVariantCounts'
eventID(x)

## S4 replacement method for signature 'SGVariants'
eventID(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
eventID(x) <- value

## S4 method for signature 'SGVariants'
variantID(x)

## S4 method for signature 'SGVariantCounts'
variantID(x)

## S4 replacement method for signature 'SGVariants'
variantID(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
variantID(x) <- value

## S4 method for signature 'SGVariants'
closed5p(x)

## S4 method for signature 'SGVariantCounts'
closed5p(x)

## S4 replacement method for signature 'SGVariants'
closed5p(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
closed5p(x) <- value

## S4 method for signature 'SGVariants'
closed3p(x)

## S4 method for signature 'SGVariantCounts'
closed3p(x)

## S4 replacement method for signature 'SGVariants'
closed3p(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
closed3p(x) <- value

## S4 method for signature 'SGVariants'
closed5pEvent(x)

## S4 method for signature 'SGVariantCounts'
closed5pEvent(x)

## S4 replacement method for signature 'SGVariants'
closed5pEvent(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
closed5pEvent(x) <- value

## S4 method for signature 'SGVariants'
closed3pEvent(x)

## S4 method for signature 'SGVariantCounts'
closed3pEvent(x)

## S4 replacement method for signature 'SGVariants'
closed3pEvent(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
closed3pEvent(x) <- value

## S4 method for signature 'SGVariants'
variantName(x)

## S4 method for signature 'SGVariantCounts'
variantName(x)

## S4 replacement method for signature 'SGVariants'
variantName(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
variantName(x) <- value

## S4 method for signature 'SGVariants'
variantType(x)

## S4 method for signature 'SGVariantCounts'
variantType(x)

## S4 replacement method for signature 'SGVariants'
variantType(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
variantType(x) <- value

## S4 method for signature 'SGVariants'
featureID5p(x)

## S4 method for signature 'SGVariantCounts'
featureID5p(x)

## S4 replacement method for signature 'SGVariants'
featureID5p(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
featureID5p(x) <- value

## S4 method for signature 'SGVariants'
featureID3p(x)

## S4 method for signature 'SGVariantCounts'
featureID3p(x)

## S4 replacement method for signature 'SGVariants'
featureID3p(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
featureID3p(x) <- value

## S4 method for signature 'SGVariants'
featureID5pEvent(x)

## S4 method for signature 'SGVariantCounts'
featureID5pEvent(x)

## S4 replacement method for signature 'SGVariants'
featureID5pEvent(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
featureID5pEvent(x) <- value

## S4 method for signature 'SGVariants'
featureID3pEvent(x)

## S4 method for signature 'SGVariantCounts'
featureID3pEvent(x)

## S4 replacement method for signature 'SGVariants'
featureID3pEvent(x) <- value

## S4 replacement method for signature 'SGVariantCounts'
featureID3pEvent(x) <- value

Arguments

x

Object containing metadata column

value

Replacement value

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.

Value

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

Author(s)

Leonard Goldstein

Examples

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

SGSeq documentation built on Nov. 8, 2020, 8:31 p.m.

Related to slots in SGSeq...

SGSeq index
Splice event prediction and quantification from RNA-seq data

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