diff --git a/404.html b/404.html index d39069b6..2e2a657d 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ RNAsum - 0.4.10 + 0.5.0.9000 + + + + + +
+
+
+

Read DRAGEN Mapping Metrics

+ Source: R/qc_dragen.R +
dragen_mapping_metrics_read.Rd
+
+ +
+

Reads the mapping_metrics.csv file output by DRAGEN.

+
+ +
+

Usage

+ 
dragen_mapping_metrics_read(x = NULL)
+
+ +
+

Arguments

+
x
+

Path to the mapping_metrics.csv file.

+ +
+
+

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
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+
+
+ + +
+ + + + + + + diff --git a/reference/empty_tbl.html b/reference/empty_tbl.html index 36151f1a..2c3e3117 100644 --- a/reference/empty_tbl.html +++ b/reference/empty_tbl.html @@ -12,7 +12,7 @@ RNAsum - 0.4.10 + 0.5.0.9000