Renders the QC report to HTML with the Quarto CLI and writes the QC output
tables (repool/reprep summaries, control summaries, filtered allele tables
and missing sample/target reports) to output_dir.
Usage
render_qc_report(
results_dir,
manifest_file,
output_dir = ".",
output_file = "QC_report.html",
panel = default_panel_settings(),
standardise_sample_name = TRUE,
read_threshold = 100,
read_filter = 0,
af_filter = 0.01,
negative_control_read_threshold = 50,
reprep_threshold = 0.5,
repool_threshold = 0.75,
allele_col = "pseudocigar_masked",
long_target_threshold = 275,
filter_wsaf_final_allele_table = TRUE,
quarto = Sys.which("quarto")
)Arguments
- results_dir
Mad4hatter results directory.
- manifest_file
Sample manifest, see
read_manifest().- output_dir
Directory for the report and output tables.
- output_file
File name of the HTML report.
- panel
Panel settings, see
panel_settings().- standardise_sample_name
If
TRUE, Illumina suffixes are removed from sample names so they match the manifest, seestandardise_illumina_sample_name(). Names already in the manifest are not changed.- read_threshold
Reads needed to count a target as successfully amplified.
- read_filter
Minimum reads per allele, for the positive control plot and the filtered allele tables.
- af_filter
Minimum within-sample allele frequency, for the positive control plot and (if
filter_wsaf_final_allele_table) the filtered allele tables.- negative_control_read_threshold
Reads above which a negative control target is reported.
- reprep_threshold
Proportion of targets amplified below which a sample needs re-prep.
- repool_threshold
Proportion of targets amplified below which a sample needs re-pool.
- allele_col
Allele ID column,
"asv"or"pseudocigar_masked".- long_target_threshold
Targets longer than this (bp, including primers) are excluded from QC.
- filter_wsaf_final_allele_table
If
FALSE, onlyread_filteris applied to the filtered allele tables.- quarto
Path to the Quarto CLI.