Reads the mapping_metrics.csv file output by DRAGEN.
Value
A tibble with the contents of the input TSV file, or NULL if input is NULL or TSV has no data rows.
Examples
x <- system.file("rawdata/test_data/dragen",
"test.mapping_metrics.csv",
package = "RNAsum"
)
(d1 <- dragen_mapping_metrics_read(x))
#> # A tibble: 113 × 6
#> category rg var var_abbrev count pct
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 summary TOTAL Total input reads reads_tot… 2.40e8 100
#> 2 summary TOTAL Number of duplicate marked reads reads_num… 0 0
#> 3 summary TOTAL Number of duplicate marked and mate … reads_num… NA NA
#> 4 summary TOTAL Number of unique reads (excl. duplic… reads_num… 2.40e8 100
#> 5 summary TOTAL Reads with mate sequenced reads_w_m… 2.40e8 100
#> 6 summary TOTAL Reads without mate sequenced reads_wo_… 0 0
#> 7 summary TOTAL QC-failed reads reads_qcf… 0 0
#> 8 summary TOTAL Mapped reads reads_map… 1.69e8 70.3
#> 9 summary TOTAL Mapped reads adjusted for filtered m… reads_map… 1.70e8 70.7
#> 10 summary TOTAL Mapped reads R1 reads_map… 8.43e7 70.3
#> # ℹ 103 more rows