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Trim methylation calls at the read ends in a mod database

Source: R/trim_mod_reads.R
trim_mod_reads.Rd

Creates a new table in a mod database that keeps only methylation calls within a central fraction of each read, optionally trimming from the start, the end, or both. Trimming is expressed as a fraction of the read length and applied via SQL filters on `read_position`.

Usage

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

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 10% of the read length from the start and/or 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").

Value

Invisibly returns the updated mod_db object, with current_table set to output_table. The function is called for its side effects of creating/replacing the trimmed table in the database.

Details

For a read of length `L` and `by_frac = f`:

  • If trim_start = TRUE, positions with read_position < L * f are dropped.

  • If trim_end = TRUE, positions with read_position >= L * (1 - f) are dropped.

For example, with read_length = 100 and by_frac = 0.1, positions 0–9 and/or 90–99 are trimmed depending on which end(s) are enabled.

This function issues a CREATE OR REPLACE TABLE SQL statement against the mod database. The resulting table contains a subset of rows from input_table where the read positions fall within the untrimmed interior region defined by by_frac, trim_start, and trim_end.

If by_frac is not strictly between 0 and 1, an error is thrown. If both trim_start and trim_end are FALSE, the function also errors, as there would be nothing to trim.

On success, mod_db$current_table is updated to output_table and a short timing message is printed.

Examples