assays: Accessing and replacing assay data

Description

Accessor and replacement functions for assay data.

Usage

FPKM(object)
FPKM(object) <- value
countsVariant5p(object)
countsVariant5p(object) <- value
countsVariant3p(object)
countsVariant3p(object) <- value
countsTotal5p(object)
countsTotal5p(object) <- value
countsTotal3p(object)
countsTotal3p(object) <- value
countsVariant(object)
countsVariant(object) <- value
countsTotal(object)
countsTotal(object) <- value
variantFreq(object)
variantFreq(object) <- value
"counts"(object)
"counts"(object) <- value
"FPKM"(object)
"FPKM"(object) <- value
"countsVariant5p"(object)
"countsVariant5p"(object) <- value
"countsVariant3p"(object)
"countsVariant3p"(object) <- value
"countsTotal5p"(object)
"countsTotal5p"(object) <- value
"countsTotal3p"(object)
"countsTotal3p"(object) <- value
"variantFreq"(object)
"variantFreq"(object) <- value
"countsVariant"(object)
"countsVariant"(object) <- value
"countsTotal"(object)
"countsTotal"(object) <- value

Arguments

object

Object containing assay data

value

Replacement value

Value

Assay data for accessor functions, updated object for replacement functions.

Details

Counts objects defined in the SGSeq package contain different types of assay data. For example, class SGFeatureCounts contains assays counts and FPKM.

To facilitate accessing and modifying assays, for each assay there exists a function with name identical to the assay name that can be used to access and modify it (see examples).

Examples

Run this code

x <- counts(sgfc)
y <- FPKM(sgfc)

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