Trim methylation calls at the read ends in a mod database

Creates a new table in a mod database that keeps only methylation calls within a central fraction of each read (i.e., trims a fraction from the start and/or end of each read).

Usage

trim_mod_reads(
  mod_db,
  by_frac = 0.1,
  trim_start = FALSE,
  trim_end = TRUE,
  input_table = "calls",
  output_table = "calls_trimmed",
  samples = NULL
)

Arguments

mod_db: An object identifying the mod database, as accepted by ModSeqR:::.modhelper_connectDB() (e.g. a file path or an existing mod database object).
by_frac: Numeric scalar between 0 and 1 (exclusive) giving the fraction of the read length to trim from each enabled end. For example, by_frac = 0.1 trims the first/last 10 on trim_start/trim_end.
trim_start: Logical; whether to trim from the start (low read_position) of each read.
trim_end: Logical; whether to trim from the end (high read_position) of each read.
input_table: Character scalar; name of the input table containing methylation calls (default "calls"). Must contain at least read_position and read_length columns.
output_table: Character scalar; name of the output table to create/overwrite with the trimmed calls (default "calls_trimmed").
samples: Character vector of sample name(s) to trim. If NULL (default), trims all samples. If non-NULL, requires a sample_name column in input_table. Only these samples are trimmed; all other samples are copied through unchanged.

Value

Invisibly returns the updated mod_db object, with current_table set to output_table.

Details

If samples is NULL (default), trimming is applied to ALL samples. If samples is provided, trimming is applied ONLY to those sample(s), and ALL rows from other samples are retained unchanged in the output table.

Examples

if (FALSE) { # \dontrun{
# Trim last 10% of reads for all samples
trim_mod_reads(mod_db, by_frac = 0.1, trim_end = TRUE, output_table = "calls_trimmed")

# Trim last 10% of reads only for Alzheimers2, keep all other samples intact
trim_mod_reads(mod_db, by_frac = 0.1, trim_end = TRUE,
               samples = "Alzheimers2", output_table = "calls_trimmed_A2")

# Trim both ends (5% each) for a subset of samples
trim_mod_reads(mod_db, by_frac = 0.05, trim_start = TRUE, trim_end = TRUE,
               samples = c("Control1", "Control2"), output_table = "calls_trimmed_controls")
} # }