alignment: Output

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

Output

Description

Do pairwise alignment for query enhancer to target genome

Usage

alignment(
  query,
  subject,
  method = c("ClustalW", "Muscle"),
  cluster = c("nj", "upgma", "upgmamax", "upgmamin", "upgmb"),
  substitutionMatrix = c("iub", "clustalw"),
  gapOpening = ifelse(method[1] == "ClustalW", 15, 400),
  gapExtension = ifelse(method[1] == "ClustalW", 6.66, 0),
  maxiters = ifelse(method[1] == "ClustalW", 3, 16),
  order = c("aligned", "input"),
  ...
)

Arguments

query	An object of DNAStringSet to represent enhancer
subject	An list of objects of Enhancers.
method	specifies the multiple sequence alignment to be used; currently, "ClustalW", and "Muscle" are supported. Default is "Muscle"
cluster	The clustering method which should be used. Possible values are "nj" (default) and "upgma". In the original ClustalW implementation, this parameter is called clustering.
substitutionMatrix	substitution matrix for scoring matches and mismatches; The valid choices for this parameter are "iub" and "clustalw". In the original ClustalW implementation, this parameter is called matrix.
gapOpening	gap opening penalty; the default is 400 for DNA sequences and 420 for RNA sequences. The default for amino acid sequences depends on the profile score settings: for the setting le=TRUE, the default is 2.9, for sp=TRUE, the default is 1,439, and for sv=TRUE, the default is 300. Note that these defaults may not be suitable if custom substitution matrices are being used. In such a case, a sensible choice of gap penalties that fits well to the substitution matrix must be made.
gapExtension	gap extension penalty; the default is 0.
maxiters	maximum number of iterations; the default is 16.
order	how the sequences should be ordered in the output object; if "aligned" is chosen, the sequences are ordered in the way the multiple sequence alignment algorithm orders them. If "input" is chosen, the sequences in the output object are ordered in the same way as the input sequences.
...	Parameters can be used by Muscle, or ClustalW.

Value

An object of Enhancers.

Examples

library(BSgenome.Hsapiens.UCSC.hg38)
library(BSgenome.Mmusculus.UCSC.mm10)
library(BSgenome.Drerio.UCSC.danRer10)
LEN <- GRanges("chr4", IRanges(19050041, 19051709))
seqEN <- getSeq(BSgenome.Drerio.UCSC.danRer10, LEN)
aln_hs <- readRDS(system.file("extdata", "aln_hs.rds",
               package="enhancerHomologSearch"))
genome(aln_hs) <- Hsapiens
aln_mm <- readRDS(system.file("extdata", "aln_mm.rds",
               package="enhancerHomologSearch"))
genome(aln_mm) <- Mmusculus
al <- alignment(seqEN, list(human=aln_hs, mouse=aln_mm),
                method="ClustalW", order="input")

jianhong/enhancerHomologSearch documentation built on Nov. 4, 2024, 8:29 p.m.