R: Masks ragged leading and trailing edges of aligned DNA...

maskSeqEnds {alakazam} | R Documentation

## Masks ragged leading and trailing edges of aligned DNA sequences

### Description

`maskSeqEnds` takes a vector of DNA sequences, as character strings, and replaces the leading and trailing characters with `"N"` characters to create a sequence vector with uniformly masked outer sequence segments.

### Usage

    maskSeqEnds(seq, mask_char = "N", max_mask = NULL, trim = FALSE)

### Arguments

`seq` | character vector of DNA sequence strings.
`mask_char` | character to use for masking.
`max_mask` | the maximum number of characters to mask. If set to 0 then no masking will be performed. If set to `NULL` then the upper masking bound will be automatically determined from the maximum number of observed leading or trailing `"N"` characters amongst all strings in `seq`.
`trim` | if `TRUE` leading and trailing characters will be cut rather than masked with `"N"` characters.

### Value

A modified `seq` vector with masked (or optionally trimmed) sequences.

### See Also

See maskSeqGaps for masking internal gaps. See padSeqEnds for padding sequence of unequal length.

### Examples

    # Default behavior uniformly masks ragged ends
    seq <- c("CCCCTGGG", "NAACTGGN", "NNNCTGNN")
    maskSeqEnds(seq)

    # Does nothing
    maskSeqEnds(seq, max_mask=0)

    # Cut ragged sequence ends
    maskSeqEnds(seq, trim=TRUE)

    # Set max_mask to limit extent of masking and trimming
    maskSeqEnds(seq, max_mask=1)
    maskSeqEnds(seq, max_mask=1, trim=TRUE)

    # Mask dashes instead of Ns
    seq <- c("CCCCTGGG", "-AACTGG-", "---CTG--")
    maskSeqEnds(seq, mask_char="-")

[Package alakazam version 0.3.0 Index]