/usr/lib/R/site-library/AnnotationDbi/unitTests/test_select.R is in r-bioc-annotationdbi 1.26.1-1.
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## - but this is fragile unless I also provide a localized example DB (which I
## probably should do anyways for other reasons, but is not necessarily useful
## here).
## Another strategy is that I should probably have tests for all my helper
## functions to make sure that they are returning what is expected.
## Generally, I want to make tests for each thing that can go wrong due to
## changes elsewhere. The strategy of writing tests for the helpers will
## catch some of this, but also I need to anticipate things that will change
## in the annotations etc.
## library(AnnotationDbi);AnnotationDbi:::.test()
require(org.Hs.eg.db)
require(org.At.tair.db)
require(org.Sc.sgd.db)
require(GO.db)
require(hgu95av2.db)
require("RUnit")
x <- org.Hs.eg.db
t <- org.At.tair.db
s <- org.Sc.sgd.db
cols <- c("CHR","PFAM","GO")
keys <- c(1,10)
jointype <- "gene_id"
quiet <- suppressWarnings # quieten warnings from 1:many mappings in select()
## resort and friends are really important as they are generic enough to
## be reused elsewhere.
test_generateExtraRows <- function(){
ttab = data.frame(warpbreaks[1:10,])
tkeys = ttab$breaks
tkeys = c(26, tkeys[1:7], tkeys[7], 30, tkeys[8:10], tkeys[10])
res <- AnnotationDbi:::.generateExtraRows(ttab, tkeys, jointype)
checkTrue(length(tkeys) == dim(res)[1])
}
test_dropUnwantedRows <- function() {
fun <- AnnotationDbi:::.dropUnwantedRows
## no duplicates, no changes
keys <- letters[1:5]
tab <- data.frame(x=keys, y=LETTERS[1:5], z=LETTERS[5:1],
row.names=NULL)
checkIdentical(tab, fun(tab, keys, "x"))
## duplicate jointype element, duplicate dropped
tab1 <- tab[c(1:5, 3L),]
rownames(tab1) <- NULL
checkIdentical(tab, fun(tab1, keys, "x"))
## unique all NA (other than jointype column) _retained_
tab1 <- tab
tab1[3, 2:3] <- NA
rownames(tab1) <- NULL
checkIdentical(tab1, fun(tab1, keys, "x"))
## duplicate all NA, made unique
tab1 <- tab
tab1[3, 2:3] <- NA
tab2 <- tab1[c(1:5, 3),]
checkIdentical(tab1, fun(tab2, keys, "x"))
## duplicate key, dropped
keys1 <- keys[c(1:5, 3)]
checkIdentical(tab, fun(tab, keys1, "x"))
}
test_resort <- function() {
fun <- AnnotationDbi:::.resort
## repeat keys returned
keys <- letters[1:5]
tab <- data.frame(x=keys, y=LETTERS[1:5], z=LETTERS[5:1],
row.names=NULL, stringsAsFactors=FALSE)
keys1 <- keys[c(1:5, 1)]
tab1 <- tab[c(1:5, 1),]
rownames(tab1) <- NULL
checkIdentical(tab1, fun(tab, keys1, "x", names(tab)))
## keys with missing values returned
tab1 <- tab
tab1[3, 2:3] <- NA
keys1 <- tab1[["x"]]
checkIdentical(tab1, fun(tab1, keys, "x", names(tab)))
## multiple keys with missing values returned
tab1 <- tab[c(3,4,3,4),]
tab1[c(1,3), 2:3] <- NA
keys1 <- keys[c(3,4,3,4)]
rownames(tab1) <- NULL
checkIdentical(tab1, fun(tab1[1:2,], keys1, "x", names(tab)))
cols <- c("CHR","SYMBOL", "PFAM")
keys <- c(1,10)
res <- AnnotationDbi:::.extractData(x, cols, keytype="ENTREZID", keys)
## jumble res to simulate trouble
resRO = res[order(sort(res$gene_id,decreasing=TRUE)),]
reqCols <- c("gene_id","chromosome","symbol","pfam_id")
Rres <- fun(resRO, keys, jointype, reqCols)
checkIdentical(Rres$gene_id,Rres$gene_id)
checkTrue(class(Rres) =="data.frame")
## now what if we have MORE keys?
keys <- c(1, keys, keys)
cols <- c("CHR","SYMBOL")
res <- AnnotationDbi:::.extractData(x, cols, keytype="ENTREZID", keys)
reqCols <- c("gene_id","chromosome","symbol")
res2 <- fun(res, keys, jointype, reqCols)
checkIdentical(as.numeric(as.character(res2$gene_id)),keys)
checkTrue(class(res) =="data.frame")
}
test_keytypes <- function(){
checkTrue("ENTREZID" %in% keytypes(x))
checkTrue("TAIR" %in% keytypes(t))
checkTrue("ENTREZID" %in% keytypes(t))
checkTrue("ORF" %in% keytypes(s))
checkTrue("ENTREZID" %in% keytypes(s))
}
test_keys <- function(){
checkException(keys(org.Hs.eg.db, keytype="PROBEID"))
egHskeys <- as.numeric(head(keys(x)))
checkTrue(length(egHskeys[!is.na(egHskeys)])==6)
rsHskeys <- head(keys(x, "REFSEQ"))
checkTrue(any(grepl("N", rsHskeys)))
egAtkeys <- as.numeric(head(keys(t,"ENTREZID")))
checkTrue(length(egAtkeys[!is.na(egAtkeys)])==6)
rsAtkeys <- head(keys(t, "REFSEQ"))
checkTrue(any(grepl("N", rsAtkeys)))
tairAtkeys <- head(keys(t, "TAIR"))
checkTrue(any(grepl("AT", tairAtkeys)))
egSckeys <- as.numeric(head(keys(s, "ENTREZID")))
checkTrue(length(egSckeys[!is.na(egSckeys)])==6)
rsSckeys <- head(keys(s, "REFSEQ"))
checkTrue(any(grepl("N", rsSckeys)))
orfSckeys <- head(keys(s, "ORF"))
checkTrue(any(grepl("A", orfSckeys)))
}
test_keys_advancedArgs <- function(){
k1 <- head(keys(x, keytype="SYMBOL"))
checkTrue("A1BG" %in% k1)
k2 <- keys(x, keytype="SYMBOL", pattern="BRCA")
checkTrue("BRCA1" %in% k2)
checkTrue(!("A1BG" %in% k2))
checkTrue(length(k2) < length(k1))
l1 <- length(keys(x, keytype="ENTREZID", column="PATH"))
l2 <- length(keys(x, keytype="ENTREZID"))
checkTrue(l1 < l2)
k3 <- keys(x,keytype="ENTREZID",pattern="^MSX",column="SYMBOL")
res <- select(x, k3, c("ENTREZID","SYMBOL"), "ENTREZID")
checkTrue(any(grep("^MSX",res$SYMBOL)))
}
#########################################################################
## These ones are to test out some real use cases...
test_select1 <- function(){
keys <- head(keys(hgu95av2.db, "ALIAS"),n=2)
cols <- c("SYMBOL","ENTREZID","PROBEID")
res <- quiet(select(hgu95av2.db, keys, cols, keytype="ALIAS"))
checkIdentical(c(3L, 4L), dim(res))
checkIdentical(c("ALIAS","SYMBOL","ENTREZID","PROBEID"), colnames(res))
}
test_select2 <- function(){
keys <- head(keys(org.Hs.eg.db),n=2)
cols <- c("PFAM","ENTREZID", "GO")
res <- quiet(select(org.Hs.eg.db, keys, cols, keytype="ENTREZID"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==5)
checkIdentical(c("ENTREZID","PFAM","GO","EVIDENCE","ONTOLOGY"),
colnames(res))
}
test_select3 <- function(){
keys <- head(keys(org.Hs.eg.db,keytype="OMIM"),n=4)
cols <- c("SYMBOL", "UNIPROT", "PATH")
res <- quiet(select(hgu95av2.db, keys, cols, keytype="OMIM"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==4)
checkIdentical(c("OMIM","SYMBOL","UNIPROT","PATH"), colnames(res))
}
test_select4 <- function(){
keys <- head(keys(org.Hs.eg.db),n=2)
cols <- c("ACCNUM","REFSEQ")
res <- quiet(select(org.Hs.eg.db, keys, cols))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ENTREZID","ACCNUM","REFSEQ"), colnames(res))
}
test_select5 <- function(){
keys <- head(keys(GO.db), n=4)
cols <- c("TERM","ONTOLOGY","DEFINITION")
res <- select(GO.db, keys, cols)
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==4)
checkIdentical(c("GOID","TERM","ONTOLOGY","DEFINITION"), colnames(res))
}
test_select6 <- function(){
keys <- head(keys(hgu95av2.db))
cols <- c("SYMBOL","ENTREZID", "GO")
## tests for bad keys:
checkException(select(hgu95av2.db, keys, cols, keytype="ENTREZID"))
## also catch bogus keytype arguments
checkException(select(hgu95av2.db, keys, cols, keytype="FOO"))
checkException(keys(hgu95av2.db, keytype="FOO"))
}
test_select7 <- function(){
cols <- c("SYMBOL","ENTREZID") ## 1st of all cols should be 1:1 cols
keys <- head(keys(org.Hs.eg.db),n=3)
keys <- c(1, keys, keys)
res <- select(org.Hs.eg.db, keys, cols)
checkTrue(class(res) =="data.frame")
checkIdentical(keys, as.character(t(res$ENTREZID)))
}
test_select8 <- function(){
cols <- c("ENTREZID")
keys <- head(keys(org.Hs.eg.db),n=3)
res <- select(org.Hs.eg.db, keys, cols)
checkTrue(class(res) =="data.frame")
checkTrue(dim(res)[2] ==1)
checkIdentical(as.character(keys), as.character(t(res$ENTREZID)))
}
test_select9 <- function(){
## What about when we need to throw away extra cols?
uniKeys <- head(keys(org.Hs.eg.db, keytype="UNIPROT"))
cols <- c("SYMBOL", "PATH")
res <- quiet(select(org.Hs.eg.db, keys=uniKeys, columns=cols, keytype="UNIPROT"))
checkTrue(class(res) =="data.frame")
checkTrue(dim(res)[2] ==3)
checkIdentical(c("UNIPROT","SYMBOL","PATH"), colnames(res))
}
test_select10 <- function(){
## What about when we have to get data from Arabidopsis using various
## keytypes?
cols <- c("SYMBOL","CHR")
keys <- head(keys(t,"TAIR"))
res <- quiet(select(t, keys, cols, keytype="TAIR"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("TAIR","SYMBOL","CHR"), colnames(res))
keys <- head(keys(t,"ENTREZID"))
res <- quiet(select(t, keys, cols, keytype="ENTREZID"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ENTREZID","SYMBOL","CHR"), colnames(res))
keys=head(keys(t,"REFSEQ"))
res <- quiet(select(t, keys, cols , keytype="REFSEQ"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("REFSEQ","SYMBOL","CHR"), colnames(res))
}
test_select11 <- function(){
## how about different keytypes for yeast?
keys <- head(keys(s, "REFSEQ"))
cols <- c("CHR","PFAM")
res <- quiet(select(s, keys, cols, keytype="REFSEQ"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("REFSEQ","CHR","PFAM"), colnames(res))
keys <- head(keys(s, "ENTREZID"))
cols <- c("CHR","PATH")
res <- quiet(select(s, keys, cols, keytype="ENTREZID"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ENTREZID","CHR","PATH"), colnames(res))
keys <- head(keys(s, "ORF"))
cols <- c("CHR","SGD")
res <- select(s, keys, cols, keytype="ORF")
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ORF","CHR","SGD"), colnames(res))
## And if you flip things the other way
cols <- c("SGD","CHR")
res <- select(s, keys, cols, keytype="ORF")
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ORF","SGD","CHR"), colnames(res))
## Martins bug discoveries
keys <- keys(s, keytype="GENENAME")
checkTrue(length(keys) > 0)
checkTrue(is.character(keys))
keys <- keys(s, keytype="CHRLOC")
checkTrue(length(keys) > 0)
checkTrue(is.character(keys))
res <- select(s, "YAL003W", "GENENAME")
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ORF","SGD","GENENAME"), colnames(res))
## This works but is slow (therefore it's tested elsewhere)
## res <- select(s, keys="YAL003W", columns(s))
## Another test to make sure we can join up to ORF properly
keys <- keys(s,"ENTREZID")
res <- select(s, columns="ORF", keys=keys, keytype="ENTREZID")
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==3)
checkIdentical(c("ENTREZID","ORF","SGD"), colnames(res))
}
test_select12 <- function(){
## what happens when we use GO as an ID?
keys <- "1"
cols <- c("GO","ENTREZID")
res <- quiet(select(x, keys, cols, keytype="ENTREZID"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==4)
checkIdentical(c("ENTREZID","GO","EVIDENCE","ONTOLOGY"), colnames(res))
keys <- "GO:0000018"
cols <- c("GO","ENTREZID")
res <- quiet(select(x, keys, cols, keytype="GO"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==4)
checkIdentical(c("GO","EVIDENCE","ONTOLOGY","ENTREZID"), colnames(res))
keys <- "GO:0000023"
cols <- c("GO","ENTREZID")
res <- quiet(select(t, keys, cols, keytype="GO"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==4)
checkIdentical(c("GO","EVIDENCE","ONTOLOGY","ENTREZID"), colnames(res))
keys <- "GO:0000023"
cols <- c("ENTREZID","TAIR","GO")
res <- quiet(select(t, keys, cols, keytype="GO"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==5)
checkIdentical(c("GO","EVIDENCE","ONTOLOGY","ENTREZID","TAIR"),
colnames(res))
}
test_select13 <- function(){
## what happens with dropping unwanted rows?
sym <- "ITGA7"
res <- quiet(select(x, sym, "PFAM", keytype="ALIAS"))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==2)
## make sure no NAs are in res$PFAM
checkTrue(length(res$PFAM)== length(res$PFAM[!is.na(res$PFAM)]))
}
test_select14 <- function(){
## what happens when there are no results AT ALL? (should be all NAs)
keys <- c("1001_at","1006_at","1007_s_at")
res <- select(hgu95av2.db, keys, "PATH", keytype="PROBEID")
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==2)
## make sure all of res$PATH ARE NAs
## If this part fails it is a warning that the test is no longer valid,
## which would happen if some of these IDs were to be further annotated for
## PATH (unlikely since PATH is basically dead for this repos)
checkTrue(length(res$PATH)== length(res$PATH[is.na(res$PATH)]))
}
test_select15 <- function(){
## Another bug that seems to happen in post-processing...
## the code that resolves duplicated values is going a bit insane...
## (IOW .replaceValues())
if(all(.Platform$OS.type == 'windows', .Platform$r_arch == 'i386')){
## Then don't do this test (you will run out of memory)
}else{
res <- select(x, keys="100008586", columns(x))
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==30)
checkIdentical(c('ENTREZID','PFAM','IPI','PROSITE','ACCNUM','ALIAS',
'CHR','CHRLOC','CHRLOCCHR','CHRLOCEND','ENZYME',
'MAP','PATH','PMID','REFSEQ','SYMBOL','UNIGENE',
'ENSEMBL','ENSEMBLPROT','ENSEMBLTRANS','GENENAME',
'UNIPROT','GO','EVIDENCE','ONTOLOGY','GOALL',
NA,'ONTOLOGYALL','OMIM','UCSCKG'),
colnames(res))
}
}
test_select16 <- function(){
## What happens if we ask for probes back...
## (and pass in something else as a key)
sk = c( 'MAPK3','TIE1' )
res <- select(hgu95av2.db, keys=sk, columns = c("PROBEID"), keytype="SYMBOL")
checkTrue(dim(res)[1]>0)
checkTrue(dim(res)[2]==2)
checkIdentical(c('SYMBOL','PROBEID'), colnames(res))
}
## TODO: figure out why in this weird corner case there is an extra col for
## GOALL called 'NA'...
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