Nothing
source('unit/setup.R')
VERBOSE <- TRUE
library(ape)
library(clstutils)
data(seqs)
data(seqdat)
# [1] "Enterococcus avium" "Enterococcus faecalis" "Enterococcus faecium"
test_refpkgContents <- function(){
contents <- refpkgContents(vag_refpkg)
checkTrue(all(c('files','md5','metadata') %in% names(contents)))
checkTrue(setequal(names(contents$files),names(contents$md5)))
}
test_taxonomyFromRefpkg01 <- function(){
taxdata <- taxonomyFromRefpkg(vag_refpkg)
## all columns should be character vectors
for(col in colnames(taxdata$taxTab)){
checkTrue(typeof(taxdata$taxTab[[col]]) == 'character')
}
with(taxdata, checkTrue(all(taxTab$tax_id %in% names(taxNames))))
## confirm that the order of taxTab reflects that of seq_info
contents <- refpkgContents(vag_refpkg)
seq_info <- read.csv(contents$files$seq_info, colClasses='character')
checkTrue(all(rownames(taxdata$taxTab) == seq_info$seqname))
}
test_findOutliers01 <- function(){
taxon <- "Enterococcus faecium"
someseqs <- seqs[seqdat$tax_name == taxon,]
somedat <- subset(seqdat, seqdat$tax_name == taxon)
checkTrue(all(rownames(someseqs) == somedat$seqname))
dmat <- dist.dna(someseqs, pairwise.deletion=TRUE, as.matrix=TRUE, model='raw')
outliers <- findOutliers(dmat, cutoff=0.015)
}
test_findOutliers02 <- function(){
taxon <- "Enterococcus faecium"
someseqs <- seqs[seqdat$tax_name == taxon,]
somedat <- subset(seqdat, seqdat$tax_name == taxon)
checkTrue(all(rownames(someseqs) == somedat$seqname))
dmat <- dist.dna(someseqs, pairwise.deletion=TRUE, as.matrix=TRUE, model='raw')
## values of quant closer to 0 are more stringent
outliers1 <- findOutliers(dmat, quant=0)
outliers2 <- findOutliers(dmat, quant=.5)
outliers3 <- findOutliers(dmat, quant=1)
checkTrue(sum(outliers1) > sum(outliers2))
checkTrue(sum(outliers2) > sum(outliers3))
}
test_maxDists01 <- function(){
taxon <- "Enterococcus faecium"
someseqs <- seqs[seqdat$tax_name == taxon,]
somedat <- subset(seqdat, seqdat$tax_name == taxon)
checkTrue(all(rownames(someseqs) == somedat$seqname))
dmat <- dist.dna(someseqs, pairwise.deletion=TRUE, as.matrix=TRUE, model='raw')
selected <- maxDists(dmat, N=1)
checkTrue(length(selected) == 1)
}
test_maxDists02 <- function(){
taxon <- "Enterococcus faecium"
someseqs <- seqs[seqdat$tax_name == taxon,]
somedat <- subset(seqdat, seqdat$tax_name == taxon)
checkTrue(all(rownames(someseqs) == somedat$seqname))
dmat <- dist.dna(someseqs, pairwise.deletion=TRUE, as.matrix=TRUE, model='raw')
selected <- maxDists(dmat, N=10)
checkTrue(length(selected) == 10)
}
test_maxDists03 <- function(){
taxon <- "Enterococcus faecium"
someseqs <- seqs[seqdat$tax_name == taxon,]
somedat <- subset(seqdat, seqdat$tax_name == taxon)
checkTrue(all(rownames(someseqs) == somedat$seqname))
dmat <- dist.dna(someseqs, pairwise.deletion=TRUE, as.matrix=TRUE, model='raw')
outliers <- findOutliers(dmat, cutoff=0.015)
selected <- maxDists(dmat, N=10, exclude=outliers)
checkTrue(length(selected) == 10)
checkTrue(all(!selected %in% seq(nrow(dmat))[outliers]))
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.