Compute Statistics for a Ch3 File — get_mod

This function computes various statistics for a given Ch3 file stored in Parquet format, including total calls, total reads, mean read length, CpG coverage at different read thresholds, flag distributions, and high-quality call counts based on probability and base quality thresholds.

Usage

get_mod_stats(
  ch3_file,
  log_file = NULL,
  min_reads = c(1, 5, 10, 15),
  call_prob_threshold = 0.9,
  base_qual_threshold = 10,
  silently = FALSE
)

Arguments

ch3_file: Character. Path to the Ch3 file in Parquet format.
log_file: Character (optional). Path to a log file where the output will be written. If NULL, results are printed to the console.
min_reads: Numeric vector. A set of thresholds for reporting CpG coverage at different minimum read counts. Default: c(1, 5, 10, 15).
call_prob_threshold: Numeric. The minimum modification probability to consider a high-confidence call. Default: 0.9.
base_qual_threshold: Numeric. The minimum base quality required to count as a high-quality call. Default: 10.
silently: Logical. If TRUE, suppresses console output. Default: FALSE.

Value

A list containing:

num_calls: Total number of modification calls in the file.
num_reads: Total number of unique reads in the file.
cpg_coverage: A matrix with CpG coverage counts at different min_reads thresholds.
flag_counts: A data frame with the count and percentage of calls per flag value.
high_conf_calls: A data frame with the count and percentage of calls with modification probability above call_prob_threshold.
high_qual_calls: A data frame with the count and percentage of calls with base quality above base_qual_threshold.
avg_read_length: The mean read length.

Details

The function reads the Ch3 file as a dataset and computes basic statistics about the calls and reads. It also evaluates CpG coverage based on different read count thresholds, distributions of flag values, and counts of high-quality calls based on user-defined probability and quality thresholds.

If a log_file is provided, the results are written to it. Otherwise, they are printed to the console unless silently = TRUE.

Examples

if (FALSE) { # \dontrun{
get_mod_stats("example.ch3.parquet")
get_mod_stats("example.ch3.parquet", log_file = "stats.log", silently = TRUE)
} # }