Validate and Normalize a BED-Format Data Frame

Validates a data frame as BED format and normalizes column names and chromosome identifiers. The function expects columns in standard BED order: chr, start, end, tag/name, score, strand.

Usage

checkBed(df)

Arguments

df

A data frame with at least 3 columns representing BED data. Columns are mapped by position: 1=chr, 2=start, 3=end, 4=tag, 5=score, 6=strand. If fewer than 6 columns are provided, missing columns are filled with defaults: tag="peak", score=0, strand="+".

Value

A validated data frame with normalized column names (chr, start, end, tag, score, strand) and chromosome names without "chr" prefix.

Details

The function performs the following:

• Requires at least 3 columns (chr, start, end)

• Maps columns by position to canonical BED names

• Fills missing columns with defaults (tag="peak", score=0, strand="+")

• Validates chromosome is character type

• Verifies end >= start for all rows

• Validates strand values are "+" or "-"

• Removes "chr" prefix from chromosome names

• Converts chromosome names to uppercase

Examples

if (FALSE) { # \dontrun{
  # Standard 6-column BED
  bed <- read.table("peaks.bed", header = FALSE)
  bed <- checkBed(bed)

  # 3-column BED (will add defaults for tag, score, strand)
  bed3 <- data.frame(chr = "chr1", start = 100, end = 200)
  bed3 <- checkBed(bed3)
} # }