Nothing
pdinfo <- pd.081229.hg18.promoter.medip.hx1
## if SNP 5.0 or 6.0, genomewide == TRUE
genomewide <- length(grep("CNV", dbListTables(db(pdinfo)))) > 0
test_table_set <- function() {
##
## this test assumes we know what tables have been defined. if we
## change the schema, this test needs to be updated
##
if (!genomewide){
alltabs.sort <- sort(c("featureSet", "mmfeature", "pm_mm", "pmfeature",
"qcmmfeature", "qcpm_qcmm", "qcpmfeature",
"sequence", "sqlite_stat1", "table_info"))
}else{
alltabs.sort <- sort(c("featureSet", "pmfeature", "sequence",
"table_info", "featureSetCNV",
"pmfeatureCNV", "sequenceCNV", "sqlite_stat1"))
}
dd <- pdinfo@getdb()
ll <- sort(dbListTables(dd))
checkEquals(alltabs.sort, ll)
}
test_table_info <- function() {
##
## this test verifies that the table_info table knows the correct
## number of rows for featureSet, and that we can get the featureSet
## table into R to count them for 50K chip this is reasonable --
## actually a little slow but maybe worth it
##
## replacing "select *" by "select fsetid" to speed up
dd <- pdinfo@getdb()
tinfo <- dbGetQuery(dd, "select * from table_info")
nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSet", "row_count" ])
fstab <- dbGetQuery(dd, "select fsetid from featureSet")
checkEquals(nrfs, nrow(fstab))
if (genomewide){
nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSetCNV", "row_count" ])
fstab <- dbGetQuery(dd, "select fsetid from featureSetCNV")
checkEquals(nrfs, nrow(fstab))
}
}
test_table_info <- function() {
##
## this test verifies that the table_info table knows the correct
## number of rows for featureSet -- commented out a table extraction
##
dd <- pdinfo@getdb()
tinfo <- dbGetQuery(dd, "select * from table_info")
nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSet", "row_count" ])
# fstab <- dbGetQuery(dd, "select * from featureSet")
nrc <- dbGetQuery(dd, "select count(*) from featureSet")[[1]]
checkEquals(nrfs, as.numeric(nrc))
if (genomewide){
nrfs <- as.numeric(tinfo[ tinfo$tbl == "featureSetCNV", "row_count" ])
fstab <- dbGetQuery(dd, "select fsetid from featureSetCNV")
checkEquals(nrfs, nrow(fstab))
}
}
test_geom <- function() {
dd <- pdinfo@getdb()
xylim = pdinfo@geometry
xs = dbGetQuery(dd, "select x from pmfeature")[[1]]
ys = dbGetQuery(dd, "select y from pmfeature")[[1]]
checkTrue(max(xs) <= xylim[2]) # zero offset?
checkTrue(max(ys) <= xylim[1]) # zero offset?
if(genomewide){
xs = dbGetQuery(dd, "select x from pmfeatureCNV")[[1]]
ys = dbGetQuery(dd, "select y from pmfeatureCNV")[[1]]
checkTrue(max(xs) <= xylim[2]) # zero offset?
checkTrue(max(ys) <= xylim[1]) # zero offset?
}
}
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