NBAMSeq-methods: Accessor functions and replace methods for NBAMSeqDataSet...

In NBAMSeq: Negative Binomial Additive Model for RNA-Seq Data

Description

Accessor functions and replace methods for NBAMSeqDataSet object

For getDesign(): accessor to the design formula

For getsf(): accessor to the size factors

Replace methods for NBAMSeqDataSet object

For setsf(): replace size factors

Usage

getDesign(theObject)

## S4 method for signature 'NBAMSeqDataSet'
getDesign(theObject)

getsf(theObject)

## S4 method for signature 'NBAMSeqDataSet'
getsf(theObject)

setsf(theObject) <- value

## S4 replacement method for signature 'NBAMSeqDataSet,numeric'
setsf(theObject) <- value

Arguments

theObject	a NBAMSeqDataSet object
value	the values to be included in the object

Value

For getDesign(): design formula

For getsf(): size factor

For setsf(): NBAMSeq object

References

Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15:550. https://doi.org/10.1186/s13059-014-0550-8

Examples

## For getDesign() ##
gsd = makeExample()
design_gsd = getDesign(gsd)
## For getsf() ##
gsd = makeExample()
sf = getsf(gsd)
## For setsf() ##
n = 100
m = 50
gsd = makeExample(n = n, m = m)
sf = sample(1:5, m, replace = TRUE)
setsf(gsd) = sf

NBAMSeq documentation built on Nov. 8, 2020, 6:26 p.m.