do_msa: Run Modified Multiple Sequence Alignment

In ShixiangWang/CNVMotif: Explore, Analyze and Visualize Catalogs and Patterns of Copy Number Variation in Cancer Genomics

Run Modified Multiple Sequence Alignment

Description

Run Modified Multiple Sequence Alignment

Usage

do_msa(
  x,
  substitutionMatrix = NULL,
  gapOpening = 6,
  gapExtension = 1,
  verbose = FALSE,
  ...
)

Arguments

x	a character vector.
substitutionMatrix	substitution matrix for scoring matches and mismatches. Default is NULL, use 1 for match and 0 for unmatch.
gapOpening	gap opening penalty; Note that the sign of this parameter is ignored.
gapExtension	gap extension penalty; Note that the sign of this parameter is ignored.
verbose	if TRUE, print extra info.
...	other arguments passing to msa::msa

Value

a list.

Examples

r <- do_msa(c("ABCDF", "BCDEF"))
r

ShixiangWang/CNVMotif documentation built on June 3, 2022, 3:44 a.m.