plyxp to compute isoform proportions

plyxp-isoform-proportions.R

library(SummarizedExperiment)

set.seed(5)

## make object ##

gene_ids <- paste0("Gene-", sprintf("%02d", 1:5))
tx_ids   <- paste0("Transcript-", sprintf("%02d", 1:20))

row_df <- data.frame(
  gene_id = rep(gene_ids, each=4),
  tx_id   = tx_ids,
  row.names = tx_ids
)

t_index <- rep(1:4, times=5)
counts <- do.call(rbind, lapply(t_index, function(t) {
  rpois(10, lambda = 100 * t)
}))
rownames(counts) <- rownames(row_df)
colnames(counts) <- paste0("Sample", sprintf("%02d", 1:10))

col_df <- data.frame(
  condition = factor(
    rep(c("control", "treated"), each=5),
    levels = c("control", "treated")
  ),
  row.names = colnames(counts)
)

se <- SummarizedExperiment(
  assays  = list(counts = counts),
  rowData = DataFrame(row_df),
  colData = col_df
)

se

## compute average isoform proportions with plyxp ##

library(plyxp)

xp <- se |> new_plyxp()

xp <- xp |> 
  group_by(rows(gene_id)) |>
  mutate(prop = t(t(counts) / colSums(counts))) |>
  ungroup()

xp_ave_prop <- xp |>
  group_by(cols(condition)) |>
  summarize(
    ave_prop = rowMeans(prop),
    cols(.samples = unique(condition))
  )

xp_ave_prop |>
  assay("ave_prop") |>
  head(4)

z <- assay(se)[1:4,1:5]
rowMeans( t(t(z) / colSums(z)) )