Comparison of DNA sequence sets, particularly when aligned.
## S3 method for class 'DNAbin' all.equal(target, current, plot = FALSE, ...)
the two sets of sequences to be compared.
a logical value specifying whether to plot the sites that are different (only if the labels of both alignments are the same).
further arguments passed to
If the two sets of DNA sequences are exactly identical, this function
TRUE. Otherwise, a detailed comparison is made only if
the labels (i.e., rownames) of
current are the
same (possibly in different orders). In all other cases, a brief
description of the differences is returned (sometimes with
recommendations to make further comparisons).
This function can be used for testing in programs using
isTRUE (see examples below).
TRUE if the two sets are identical; a list with two elements
(message and different.sites) if a detailed comparison is done; or a
vector of mode character.
the generic function:
data(woodmouse) woodm2 <- woodmouse woodm2[1, c(1:5, 10:12, 30:40)] <- as.DNAbin("g") res <- all.equal(woodmouse, woodm2, plot = TRUE) str(res) ## if used for testing in R programs: isTRUE(all.equal(woodmouse, woodmouse)) # TRUE isTRUE(all.equal(woodmouse, woodm2)) # FALSE all.equal(woodmouse, woodmouse[15:1, ]) all.equal(woodmouse, woodmouse[-1, ]) all.equal(woodmouse, woodmouse[, -1]) ## Not run: ## To run the followings you need internet and Clustal and MUSCLE ## correctly installed. ## Data from Johnson et al. (2006, Science) refs <- paste("DQ082", 505:545, sep = "") DNA <- read.GenBank(refs) DNA.clustal <- clustal(DNA) DNA.muscle <- muscle(DNA) isTRUE(all.equal(DNA.clustal, DNA.muscle)) # FALSE all.equal(DNA.clustal, DNA.muscle, TRUE) ## End(Not run)
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