Package: r-bioc-variantannotation / 1.20.2-1

drop_tests_requiring_large_data_sets.patch Patch series | download
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Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 24 Jul 2014 08:35:54 +0200
Description: Make test independent from TxDb.Hsapiens.UCSC.hg19.knownGene
 and other not packaged databases (see debian/README.test)

--- a/inst/unitTests/test_locateVariants-methods.R
+++ /dev/null
@@ -1,136 +0,0 @@
-library(TxDb.Hsapiens.UCSC.hg19.knownGene)
-txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene 
-cdsbytx <- cdsBy(txdb, use.names=TRUE)
-intbytx <- intronsByTranscript(txdb)
-txbygene <- transcriptsBy(txdb, "gene")
-
-gr <- GRanges("chr22", 
-    IRanges(c(16268137, 16287254, 16190792, 16164570,
-              18209442, 18121652, 24314750, 25508661), 
-            width=c(1,1,1,1,3,3,2,2)),
-    strand=c("-", "-", "-", "+", "+", "+", "+", "+"))
-
-test_locateVariants_upstream_downstream <- function()
-{
-    loc <- locateVariants(gr, txdb, IntergenicVariants(1, 1))
-    target <- CharacterList(character(), character())
-    checkIdentical(loc$FOLLOWID, target)
-
-    loc <- locateVariants(gr, txbygene, IntergenicVariants(2, 2))
-    target <- CharacterList(character(), "100037417")
-    checkIdentical(loc$FOLLOWID, target) 
-
-    loc <- locateVariants(gr, txbygene, IntergenicVariants(100000, 100000))
-    target <- CharacterList("23784", c("100037417","4282", "66035"))
-    checkIdentical(loc$FOLLOWID, target)
-    target <- CharacterList(character(), c("23523", "2953", "391322"))
-    checkIdentical(loc$PRECEDEID, target)
-}
-
-test_locateVariants_queryAsVCF <- function()
-{
-    fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
-    vcf <- readVcf(fl, "hg19")
-    vcf <- renameSeqlevels(vcf, c("1" = "chr1"))
-    loc1 <- locateVariants(vcf, txdb, IntergenicVariants())
-    loc2 <- locateVariants(rowRanges(vcf), txdb, IntergenicVariants())
-    checkIdentical(loc1, loc2) 
-}
-
-test_locateVariants_ignore.strand <- function()
-{
-    cdsbytx <- cdsbytx[1:5]
-    gr <- GRanges("chr1", IRanges(c(12190, 12595, 13403), width=1), "-")
-    loc1 <- locateVariants(gr, cdsbytx, CodingVariants(), 
-                           ignore.strand=TRUE)
-    checkIdentical(c(1L, 2L, 3L), mcols(loc1)$QUERYID) 
-    loc2 <- locateVariants(gr, cdsbytx, CodingVariants(), 
-                           ignore.strand=FALSE)
-    checkIdentical(integer(), mcols(loc2)$QUERYID) 
-    loc1 <- locateVariants(gr, cdsbytx, SpliceSiteVariants(), 
-                           ignore.strand=TRUE)
-    checkIdentical(c(1L, 2L, 3L), mcols(loc1)$QUERYID) 
-    loc2 <- locateVariants(gr, cdsbytx, SpliceSiteVariants(), 
-                           ignore.strand=FALSE)
-    checkIdentical(integer(), mcols(loc2)$QUERYID) 
-}
-
-test_locateVariants_asHits <- function()
-{
-    gr <- GRanges("chr1", IRanges(c(12190, 69091, 13403), width=1))
-    loc <- locateVariants(gr, cdsbytx, CodingVariants())
-    hit <- locateVariants(gr, cdsbytx, CodingVariants(), asHits=TRUE)
-    ## annotation element 
-    loc_nms <- as.character(mcols(loc)$TXID)
-    hit_nms <- names(cdsbytx[subjectHits(hit)])
-    checkIdentical(loc_nms, hit_nms) 
-
-    ## Hits lengths
-    checkIdentical(length(gr), queryLength(hit))
-    checkIdentical(length(cdsbytx), subjectLength(hit))
-}
-
-.extract <- function(x, col) as.vector(mcols(x)[[col]])
-test_locateVariants_PromoterVariants <- function()
-{
-    s <- GRangesList(GRanges("chr1", IRanges(10, width=11), "+"),
-                     GRanges("chr1", IRanges(30, width=11) , "+"))
-    ## empty 
-    q <- GRanges("chr1", IRanges(15, width=1), "+")
-    current <- locateVariants(q, s, PromoterVariants(5, 5))
-    checkTrue(length(current) == 0)
- 
-    ## endpoint
-    q <- GRanges("chr1", IRanges(20, width=1), "+")
-    current <- locateVariants(q, s, PromoterVariants(5, 5))
-    checkTrue(length(current) == 0)
- 
-    ## strand 
-    q <- GRanges(c("chr1", "chr1"), IRanges(c(8, 12), width=1), "+")
-    current <- locateVariants(q, s, PromoterVariants(5, 5))
-    checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
-    strand(s) <- RleList(Rle(factor("*")), Rle(factor("*")))
-    strand(q) <- "*"
-    current <- suppressWarnings(locateVariants(q, s, PromoterVariants(5, 5)))
-    checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
-    q <- GRanges(c("chr1", "chr1"), IRanges(c(21, 41), width=1), "-")
-    strand(s) <- RleList(Rle(factor("-")), Rle(factor("-")))
-    current <- locateVariants(q, s, PromoterVariants(5, 5))
-    checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
-
-    q <- GRanges(c("chr2", "chr2"), IRanges(c(9, 10), width=1), "+")
-    s <- GRangesList(GRanges("chr2", IRanges(10, width=11), "+"))
-    current <- locateVariants(q, s, PromoterVariants(5, 0))
-    checkEquals(1L, .extract(current, "QUERYID"))
-    current <- locateVariants(q, s, PromoterVariants(5, 1))
-    checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
-    current <- locateVariants(q, s, PromoterVariants(0, 0))
-    checkTrue(length(current) == 0L)
-
-    q <- GRanges("chr22", IRanges(50310410, 50310420))
-    current <- locateVariants(q, txdb, PromoterVariants())
-    checkIdentical(unique(current$GENEID), "79174")
-}
-
-test_locateVariants_match_predictCoding <- function()
-{
-    library(BSgenome.Hsapiens.UCSC.hg19)
-    gr <- GRanges("chr20", IRanges(
-        start=c(77055, 77054, 77054, 77058, 77057, 77057, 77055), 
-        end=c(77055, 77055, 77055, 77058, 77058, 77058, 77054)),
-        paramRangeID=rep(NA, 7))
-    fixed <- DataFrame(
-        REF=DNAStringSet(c('T', 'AT', 'AT', 'A', 'AA', 'AA', 'T')), 
-        ALT=DNAStringSetList('G', 'A', 'ATT', 'G', 'A', 'AAT', 'G'), 
-        QUAL=70, FILTER="PASS")
-    vcf <- VCF(rowRanges=gr, fixed=fixed)
-
-    ## coding regions match, zero-width
-    loc <- locateVariants(vcf, txdb, CodingVariants())
-    coding <- predictCoding(vcf, txdb, Hsapiens)
-    checkIdentical(loc$QUERYID, as.integer(1:7))
-    checkIdentical(length(coding) , 6L)
-    checkIdentical(loc$CDSID[1:6], coding$CDSID)
-    checkIdentical(unname(as.character(coding$VARCODON[c(1,4)])), 
-                   as.character(DNAStringSet(c("AAG", "TAG"))))
-}
--- a/inst/unitTests/test_SIFTandPolyPhen.R
+++ /dev/null
@@ -1,39 +0,0 @@
-library(SIFT.Hsapiens.dbSNP132)
-library(PolyPhen.Hsapiens.dbSNP131)
-quiet <- suppressWarnings
-
-test_SIFT_132 <- function()
-{
-    db <- SIFT.Hsapiens.dbSNP132
-    scol <- columns(db)
-    checkIdentical(length(scol), 10L) 
-
-    res <- select(db, "rs2142947")
-    checkIdentical(nrow(res), 4L)
-
-    res <- select(db, "rs2142947", columns="AACHANGE")
-    checkIdentical(nrow(res), 1L)
-
-    res <- 
-      quiet(select(db, keys=c("rs17970171", "INVALID", "rs17970171")))
-    checkIdentical(nrow(res), 9L)
-    checkTrue(all(res$RSID %in% c("rs17970171", "INVALID"))) 
-}
-
-test_PolyPhen <- function()
-{
-    db <- PolyPhen.Hsapiens.dbSNP131
-    pcol <- columns(db)
-    checkIdentical(length(pcol), 58L) 
-
-    res <- select(db, "rs3026284")
-    checkIdentical(nrow(res), 2L)
-
-    res <- select(db, "rs3026284", columns="POS")
-    checkIdentical(nrow(res), 1L)
-
-    res <- 
-      suppressWarnings(select(db, keys=c("rs3026284", "INVALID", "rs3026284")))
-    checkIdentical(nrow(res), 5L)
-    checkTrue(all(res$RSID %in% c("rs3026284", "INVALID"))) 
-}
--- a/inst/unitTests/test_predictCoding-methods.R
+++ /dev/null
@@ -1,111 +0,0 @@
-quiet <- suppressWarnings
-library(BSgenome.Hsapiens.UCSC.hg19)
-fun <- VariantAnnotation:::.predictCodingGRangesList
-cdsbytx <- GRangesList(tx1=GRanges(seqnames="chr1", 
-                                   IRanges(c(10001, 10010), width=5), 
-                                   strand="+"),
-                       tx2=GRanges(seqnames="chr1", 
-                                   IRanges(c(10100, 10001), width=5), 
-                                   strand="-"),
-                       tx3=GRanges(seqnames="chr1", 
-                                   IRanges(c(10010, 10001), width=5), 
-                                   strand="-"))
-
-test_predictCoding_empty <- function()
-{
-    query <- GRanges("chr1", IRanges(start=c(1, 10, 20), width=1))
-    current <- fun(query, cdsbytx, Hsapiens, DNAStringSet(c("G", "T", "A")))
-    checkIdentical(dim(mcols(current)), c(0L, 8L))
-}
-
-test_predictCoding_varAllele <- function()
-{
-    variant=DNAStringSet(c("G", "", "C", "AA", "GGA"))
-    query <- GRanges(seqnames="chr1",
-              ranges=IRanges(c(rep(10003, 3), 10011, 10101), 
-                             width=c(1, 1, 1, 2, 3)),
-              strand=c("+", "-", "*", "*", "*"),
-              variant=variant)
-    names(query) <- LETTERS[1:5]
-    current <- quiet(fun(query, cdsbytx[1:2], Hsapiens, variant))
-
-    current_varaa <- values(current[names(current) == "B"])[["VARAA"]]
-    checkTrue(as.character(current_varaa) == "")
-
-    current_consequence <- 
-      values(current[names(current) == "B"])[["CONSEQUENCE"]]
-    checkTrue(current_consequence == "not translated")
-
-    variant=DNAStringSet(c("GGA", "GGA"))
-    query <- GRanges("chr1", IRanges(rep(10101, 2), width=c(2,3)), 
-                     variant=variant)
-    current <- quiet(fun(query, cdsbytx[1:2], Hsapiens, variant))
-    checkIdentical(unname(as.character(mcols(current)$VARCODON)), 
-                   c("TATCCGG", "TTCCGG"))
-}
-
-test_mapToTranscripts <- function()
-{
-    ## both in 'first' cds
-    query <- GRanges(seqnames="chr1",
-              ranges=IRanges(rep(c(10002, 10005), 2), width=1),
-              strand=c("+", "+", "-", "-"))
-    current <- mapToTranscripts(query, cdsbytx[c(1,3)], ignore.strand=FALSE)
-    expected <- IRanges(c(2, 5, 9, 6), width=1) 
-    checkIdentical(ranges(current), expected)
-
-    ## one in each cds
-    query <- GRanges(seqnames="chr1",
-                     ranges=IRanges(rep(c(10002, 10011), 2), width=1),
-                     strand=c("+", "+", "-", "-"))
-    current <- mapToTranscripts(query, cdsbytx[c(1,3)], ignore.strand=FALSE)
-    expected <- IRanges(c(2, 7, 9, 4), width=1) 
-    checkIdentical(ranges(current), expected)
-
-    ## both in 'last' cds
-    query <- GRanges(seqnames="chr1",
-                     ranges=IRanges(rep(c(10010, 10013), 2), width=1),
-                     strand=c("+", "+", "-", "-"))
-    current <- mapToTranscripts(query, cdsbytx[c(1,3)], ignore.strand=FALSE)
-    expected <- IRanges(c(6, 9, 5, 2), width=1) 
-    checkIdentical(ranges(current), expected)
-} 
-
-test_predictCoding_strand <- function()
-{
-    variant=DNAStringSet(c("G", "G", "C", "T", "G"))
-    query <- GRanges(seqnames="chr1",
-              ranges=IRanges(c(rep(10003, 3), 10011, 10101), width=1),
-              strand=c("+", "-", "*", "*", "*"),
-              variant=variant)
-    names(query) <- LETTERS[1:5]
-
-    current <- quiet(fun(query, cdsbytx, Hsapiens, variant))
-    expected <- c("G", "C", "C", "C", "G", "G", "T", "A", "C")
-    checkIdentical(as.character(mcols(current)$varAllele), expected)
-
-    ## query "+", subject "-"
-    v <- variant[2]
-    q <- query[2]
-    strand(q) <- "+"
-    s <- cdsbytx[3]
-    current <- quiet(fun(q, s,  Hsapiens, v, ignore.strand=FALSE))
-    checkIdentical(length(current), 0L)
-
-    current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=TRUE))
-    checkIdentical(as.character(mcols(current)$REFAA), "V")
-    checkIdentical(as.character(mcols(current)$VARAA), "A")
-    checkIdentical(mcols(current)$CDSLOC, IRanges(8, 8))
-
-    ## query "-", subject "+"
-    strand(q) <- "-"
-    s <- cdsbytx[1]
-    current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=FALSE))
-    checkIdentical(length(current), 0L)
-
-    current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=TRUE))
-    checkIdentical(as.character(mcols(current)$REFAA), "*")
-    checkIdentical(as.character(mcols(current)$VARAA), "*")
-    checkIdentical(mcols(current)$CDSLOC, IRanges(3, 3))
-}
-