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Calculate Illumina Summary Statistics

illumina_summary_stats.Rd

Processes Illumina quality metrics data to calculate median quality scores for specified samples.

Usage

illumina_summary_stats(path = NULL, sample_ids = NULL)

Arguments

path

Character. Path to the Illumina Quality_Metrics.csv file.

sample_ids

Character vector. Sample IDs to filter and analyze.

Value

A data frame with columns:

SampleID

Sample identifier

mu_pf

Median Mean Quality Score (PF) for each sample

mu_q30

Median percentage of Q30 bases for each sample

Details

This function reads Illumina sequencing quality metrics and calculates median values for two key quality indicators:

  • Mean Quality Score (PF): Quality score for reads passing filter

  • % Q30: Percentage of bases with quality score ≥30 (99.9% accuracy)

Examples

if (FALSE) { # \dontrun{
stats <- illumina_summary_stats(
  path = "path/to/Quality_Metrics.csv",
  sample_ids = c("Sample1", "Sample2", "Sample3")
)
} # }