assays: Accessing and replacing assay data

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

Description

Functions counts and FPKM are used to extract counts and FPKM values from SGFeatureCounts and SGVariantCounts objects. Function variantFreq is used to access relative usage estimates from SGVariantCounts objects.

Usage

FPKM(object, ...)

FPKM(object, ...) <- value

variantFreq(object)

variantFreq(object) <- value

## S4 method for signature 'SGFeatureCounts'
counts(object)

## S4 replacement method for signature 'SGFeatureCounts'
counts(object) <- value

## S4 method for signature 'SGFeatureCounts'
FPKM(object)

## S4 replacement method for signature 'SGFeatureCounts'
FPKM(object) <- value

## S4 method for signature 'SGVariantCounts'
counts(object, ...)

## S4 replacement method for signature 'SGVariantCounts'
counts(object, ...) <- value

## S4 method for signature 'SGVariantCounts'
FPKM(object, ...)

## S4 method for signature 'SGVariantCounts'
variantFreq(object)

## S4 replacement method for signature 'SGVariantCounts'
variantFreq(object) <- value

Arguments

object	Object containing assay data
...	Arguments passed to method for SGVariantCounts objects. Argument option specifies whether the output should be based on the count of fragments compatible with the variant at the start (“variant5p”), end (“variant3p”) or either (“variant5pOr3p”) (the default), or whether output should be based on the count of fragments compatible with any variant belonging to the same event (“event5p” or “event3p”). Argument min_anchor specifies the minimum anchor length when computing FPKM values (defaults to 1).
value	Replacement value

Value

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

Author(s)

Leonard Goldstein

Examples

x <- counts(sgfc_pred)
y <- FPKM(sgfc_pred)
u <- counts(sgvc_pred, option = "variant5p")
v <- FPKM(sgvc_pred, option = "variant5p")

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.