## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = '#>',
  message = FALSE,
  fig.align = 'center',
  fig.retina = 2,
  eval = FALSE)

foreach::registerDoSEQ()

## -----------------------------------------------------------------------------
# library('limorhyde2')
# # txi = ?
# # metadata = ?

## -----------------------------------------------------------------------------
# keep = rowSums(edgeR::cpm(txi$counts) >= 0.5) / ncol(txi$counts) >= 0.75
# 
# txiKeep = txi
# for (name in c('counts', 'length')) {
#   txiKeep[[name]] = txi[[name]][keep, ]}

## -----------------------------------------------------------------------------
# for (i in seq_len(nrow(txiKeep$counts))) {
#   idx = txiKeep$counts[i, ] > 0
#   txiKeep$counts[i, !idx] = min(txiKeep$counts[i, idx])}

## -----------------------------------------------------------------------------
# y = edgeR::DGEList(txiKeep$counts)
# y = edgeR::calcNormFactors(y)
# 
# fit = getModelFit(y, metadata, ..., method = 'voom') # replace '...' as appropriate for your data

## -----------------------------------------------------------------------------
# y = DESeq2::DESeqDataSetFromTximport(txiKeep, metadata, ~1)
# 
# fit = getModelFit(y, metadata, ..., method = 'deseq2') # replace '...' as appropriate for your data