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 x 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