maskSeqGaps: Masks gap characters in DNA sequences

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Masks gap characters in DNA sequences

Description

maskSeqGaps substitutes gap characters, c("-", "."), with "N" in a vector of DNA sequences.

Usage

maskSeqGaps(seq, mask_char = "N", outer_only = FALSE)

Arguments

seq	character vector of DNA sequence strings.
mask_char	character to use for masking.
outer_only	if TRUE replace only contiguous leading and trailing gaps; if FALSE replace all gap characters.

Value

A modified seq vector with "N" in place of c("-", ".") characters.

See Also

See maskSeqEnds for masking ragged edges.

Examples

# Mask with Ns
maskSeqGaps(c("ATG-C", "CC..C"))
maskSeqGaps("--ATG-C-")
maskSeqGaps("--ATG-C-", outer_only=TRUE)

# Mask with dashes
maskSeqGaps(c("ATG-C", "CC..C"), mask_char="-")

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.