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Add gene-level 'obs_raw' support to 'sleuth_to_matrix' #189

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Add gene-level 'obs_raw' support to 'sleuth_to_matrix' #189

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14 changes: 8 additions & 6 deletions R/matrix.R
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Original file line number Diff line number Diff line change
Expand Up @@ -40,12 +40,6 @@ sleuth_to_matrix <- function(obj, which_df, which_units) {

which_units <- check_quant_mode(obj, which_units)

if (obj$gene_mode && which_df == "obs_raw") {
warning("This object is in gene mode, and the raw values are ",
"transcripts. Using 'obs_norm' instead.")
which_df <- "obs_norm"
}

data <- as.data.frame(obj[[which_df]])

res <- list()
Expand All @@ -56,5 +50,13 @@ sleuth_to_matrix <- function(obj, which_df, which_units) {
s_data$target_id <- NULL
s_data <- as.matrix(s_data)

if (obj$gene_mode && which_df == "obs_raw") {
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@mschilli87 mschilli87 Jun 27, 2018

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Maybe you still want to issue a warning here to make sure the user understand the drawbacks of what he's doing? 😉

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@apcamargo apcamargo Jun 27, 2018

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Sure! I think this is a nice idea to expose the drawbacks.
What do you think that should be warned here?

  • scaled_reads_per_base is a artificial measure to represent the read counts of genes (in this case, the same warning appear when the user requests obs_norm).
  • The raw values of scaled_reads_per_base are not normalized and, therefore, should not be directly compared.

if (which_units == "scaled_reads_per_base") {
s_data <- t(t(s_data)*obj$est_counts_sf)
} else {
s_data <- t(t(s_data)*obj$tpm_sf)
}
}

s_data
}