Add gene-level 'obs_raw' support to 'sleuth_to_matrix'#189
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apcamargo wants to merge 1 commit intopachterlab:masterfrom
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Add gene-level 'obs_raw' support to 'sleuth_to_matrix'#189apcamargo wants to merge 1 commit intopachterlab:masterfrom
apcamargo wants to merge 1 commit intopachterlab:masterfrom
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mschilli87
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Jun 27, 2018
| s_data$target_id <- NULL | ||
| s_data <- as.matrix(s_data) | ||
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| if (obj$gene_mode && which_df == "obs_raw") { |
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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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Sure! I think this is a nice idea to expose the drawbacks.
What do you think that should be warned here?
scaled_reads_per_baseis a artificial measure to represent the read counts of genes (in this case, the same warning appear when the user requestsobs_norm).- The raw values of
scaled_reads_per_baseare not normalized and, therefore, should not be directly compared.
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I added gene-level
obs_rawsupport tosleuth_to_matrixby multiplying the normalized matrix by the size factors if the user request non-normalized values.