Sample- and gene-level summaries computed from the RSEM expected counts and TPM. A gene is "detected" when its expected count is above zero. These are descriptive numbers only; no sample is flagged or removed.
Examples
ex <- system.file("extdata", "example", package = "rsemflow")
study <- read_rsem_study(file.path(ex, "data"), file.path(ex, "metadata.tsv"))
s <- summarize_study(study)
s$samples
#> sample_id total_expected_count detected_genes undetected_genes
#> C1 C1 21880 200 0
#> C2 C2 21970 200 0
#> C3 C3 21960 200 0
#> D1 D1 27225 200 0
#> D2 D2 26585 200 0
#> D3 D3 26765 200 0
#> detected_fraction tpm_q25 tpm_median tpm_q75 tpm_sum
#> C1 1 2619.979 4326.391 6689.095 1e+06
#> C2 1 2636.108 4416.054 6665.577 1e+06
#> C3 1 2628.449 4448.008 6661.793 1e+06
#> D1 1 1477.125 3068.127 5310.146 1e+06
#> D2 1 1511.890 3073.025 5360.227 1e+06
#> D3 1 1479.227 2939.596 5321.024 1e+06