R: Masks gap characters in DNA sequences

maskSeqGaps {alakazam} | R Documentation

## 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="-")

[Package alakazam version 0.3.0 Index]