brentlabRnaSeqSet object and constructor

A container for expression data in brentlab rnaseq databases

Usage

brentlabRnaSeqSet(dds = NULL)

brentlabRnaSeqSetFromDatabase(
  organism,
  username,
  password,
  full_rnaseq_only = TRUE
)

Arguments

dds

a deseq data object. Passing a null object will instantiate with the DESeq2::makeExampleDESeqDataSet

organism

currently, only kn99

username

db username

password

db password

full_rnaseq_only

filter out spikeins before returning. Default TRUE

Value

a brentlabRnaSeqSet for the given organism

See also

• extending DESeqDataSet

• extending SummarizedExperiment. Note that A SummarizedExperiment object becomes a RangedSummarizedExperiment object when rowRanges are added.