maskSeqGaps - 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.

Examples¶

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

[1] "ATGNC" "CCNNC"

maskSeqGaps("--ATG-C-")

[1] "NNATGNCN"

maskSeqGaps("--ATG-C-", outer_only=TRUE)

[1] "NNATG-CN"

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

[1] "ATG-C" "CC--C"

See also¶

See maskSeqEnds for masking ragged edges.