alakazam (version 0.2.2)

maskSeqGaps: Masks gap characters in DNA sequences

Description

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

Usage

maskSeqGaps(seq, outer_only = FALSE)

Arguments

seq

a character vector of DNA sequence strings.

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

Other sequence manipulation functions: collapseDuplicates, maskSeqEnds

Examples

maskSeqGaps(c("ATG-C", "CC..C"))
maskSeqGaps("--ATG-C-")
maskSeqGaps("--ATG-C-", outer_only=TRUE)