tests/testthat/test_queryFunctions.R
In BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements
# ----------------------------------------------------------------------------
# Unitests for query functions
#########################
# Create test datasets
library(InteractionSet)
library(testthat)
library(GenomicRanges)
library(genomation)
library(reg2gene)
# Create windows
windows <- GRanges(c("chr1:1-2", # 1. overlap prom
"chr2:1-2", # 2. overlap enh
"chr3:1-2", # 3. overlap tss +/- 1,000,000
"chr4:1-2")) # 4. do not overlap tss +/- 1Mb
annotationsEnh <- GRanges(c("chr1:1-2",
"chr2:1-2",
"chr3:100000-100002",
"chr4:10000001-10000002"))
annotationsGenes <- GRanges(c("chr1:1-2",
"chr2:100000-100002",
"chr3:99999-100002",
"chr4:10000001-10000002"))
seqlengths(annotationsEnh) <- seqlengths(annotationsGenes) <- rep(10000002,
4)
interactions = GInteractions(annotationsEnh,annotationsGenes,
name=c("gen1","gen2","gen3","gen4"))
geneAnnotations=second(interactions)
mcols(geneAnnotations) <- mcols(interactions)
# Planned combinations
# 1) intset NULL, geneA 1 #expO: gen1
# 2) intset full, geneA 1 #expO: gen1,gen2
# 3) intset full, geneA full #expO: gen1,gen2,gen3
# 4) intset full, geneA 1&3 #expO: gen1,gen2,gen3
# 5) intset full -2 , geneA full #expO: gen1,gen3
# 6) intset 4, geneA 4 no overlap identified
# Combinations when intset does not contain info about gene, whereas
# it needs to be infered from geneAnnotations
# 7) intset full, geneA 1
# 8) intset full, geneA full
# 9) ? intset full, geneA full
################################################
####### TEST annotatewindows
test_that("annotatewindows INPUT/OUTPUT is correct in form",{
# TEST INPUT:
expect_true(class(windows)=="GRanges")
expect_true(class(geneAnnotations)=="GRanges")
expect_true(class(interactions)=="GInteractions")
# test expected input meta-data:
expect_equal(colnames(mcols(interactions)),"name")
expect_equal(colnames(mcols(geneAnnotations)),"name")
# TEST OUTPUT - QFR
# is GRanges with lenght>0
QFR <- reg2gene(windows = windows,
interactions=interactions,
geneAnnotations = geneAnnotations)
expect_is(QFR,"GInteractions")
expect_equal(names(mcols(QFR)),c("name","annotatedAs"))
# if interactions is NULL is GRanges object - works ok
QFR <- reg2gene(windows = windows,
interactions=NULL,
geneAnnotations = geneAnnotations)
expect_is(QFR,"GInteractions")
expect_equal(names(mcols(QFR)),c("name","annotatedAs"))
# if interactions have no info about gene - just geneAnnot have info
interactions2 <- interactions
mcols(interactions2) <- NULL
QFR <- reg2gene(windows = windows,
interactions=interactions2,
geneAnnotations = geneAnnotations,
annotateInteractions = TRUE)
expect_is(QFR,"GInteractions")
expect_equal(names(mcols(QFR)),c("name","annotatedAs"))
})
test_that("reg2gene arguments are correctly used",{
# 1) intset NULL, geneA 1 #expO: gen1
QFR <- reg2gene(windows = windows,
interactions = NULL,
geneAnnotations = geneAnnotations[1])
expect_equal(length(QFR),1)
expect_equal(QFR$name,"gen1")
expect_equal(granges(second(QFR)),granges(geneAnnotations[1]))
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = NULL,
geneAnnotations = geneAnnotations[1],
identified = FALSE), windows[-1])
# 2) intset full, geneA 1 #expO: gen1,gen2
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1])
expect_equal(length(QFR),2) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","enhancer"))
expect_false("gen4"%in%QFR$name)
expect_false("gen3"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1],
identified = FALSE), windows[3:4])
# 3) intset full, geneA full #expO: gen1,gen2,gen3
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations)
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene","enhancer"))
expect_false("gen4"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
identified = FALSE), windows[4])
# 4) intset full, geneA 1&3 #expO: gen1,gen2,gen3
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations[c(1,3)])
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene","enhancer"))
expect_false("gen4"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
identified = FALSE), windows[4])
# 5) intset full -2 , geneA full #expO: gen1,gen3
QFR <- reg2gene(windows,
interactions = interactions[-2],
geneAnnotations = geneAnnotations)
# Enhancer missing, but promoter failed as well
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2","gen3"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene","nearestGene"))
expect_false("gen4"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
identified = FALSE), windows[4])
# 5)a intset full -2 , geneA -2 #expO: gen1,gen3
QFR <- reg2gene(windows,
interactions = interactions[-2],
geneAnnotations = geneAnnotations[-2])
# 5a Enhancer missing, but promoter failed as well
expect_equal(length(QFR),2) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene"))
expect_false("gen4"%in%QFR$name)
expect_false("gen2"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions[-2],
geneAnnotations = geneAnnotations[-2],
identified = FALSE), windows[c(2,4)])
# 6) intset 4, geneA 4 - no overlap identified
QFR <- reg2gene(windows,
interactions = interactions[4],
geneAnnotations = geneAnnotations[4])
expect_equal(QFR,"No overlap identified!")
# check identified=F argument
expect_equal(reg2gene(windows,
interactions = interactions[4],
geneAnnotations = geneAnnotations[4],
identified = FALSE),windows)
# test distance +/-10000000
# increase distance works well
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 10000000)
expect_equal(length(QFR),4) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3","gen4","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene",
"nearestGene","enhancer"))
expect_true("gen4"%in%QFR$name)
expect_equal(length(reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 10000000,identified = FALSE)),0)
# reduce distance -/+ 100
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 100)
expect_equal(length(QFR),2) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","enhancer"))
expect_false("gen4"%in%QFR$name)
expect_false("gen3"%in%QFR$name)
expect_equal(length(reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 100,identified = FALSE)),2)
# upstream,downstream [+/-1bp]
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
downstream = 1,
upstream = 1,
distance = 100)
expect_equal(length(QFR),2) # 2 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2"))
# but if distance is 1MB,then the 3rd gene should be identified as well
expect_equal( reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
downstream = 1, upstream = 100000,
distance = 100)$name,c("gen1","gen2",
"gen3"))
#################################################################
# ---------------------------------------------------------------
# 7) intset full, geneA 1
mcols(interactions) <- NULL
QFR <- reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1],
annotateInteractions = TRUE)
expect_equal(length(QFR),1)
expect_equal(QFR$name,"gen1")
expect_equal(granges(second(QFR)),granges(geneAnnotations[1]))
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = NULL,
geneAnnotations = geneAnnotations[1],
identified = FALSE,
annotateInteractions = TRUE),
windows[-1])
# if annotateInteractions needed to be TRUE, but it is not
# defined
expect_true(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1])==
"ERROR! Try setting annotateInteractions = TRUE")
# 8) intset full, geneA full
QFR <- reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
annotateInteractions = TRUE)
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2","gen3"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,
c("promoter","nearestGene","nearestGene"))
expect_false("gen4"%in%QFR$name)
# if annotateInteractions needed to be TRUE, but it is not
# defined
expect_true(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations)==
"ERROR! Try setting annotateInteractions = TRUE")
})
BIMSBbioinfo/reg2gene documentation built on May 3, 2019, 6:42 p.m.
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# ----------------------------------------------------------------------------
# Unitests for query functions
#########################
# Create test datasets
library(InteractionSet)
library(testthat)
library(GenomicRanges)
library(genomation)
library(reg2gene)
# Create windows
windows <- GRanges(c("chr1:1-2", # 1. overlap prom
"chr2:1-2", # 2. overlap enh
"chr3:1-2", # 3. overlap tss +/- 1,000,000
"chr4:1-2")) # 4. do not overlap tss +/- 1Mb
annotationsEnh <- GRanges(c("chr1:1-2",
"chr2:1-2",
"chr3:100000-100002",
"chr4:10000001-10000002"))
annotationsGenes <- GRanges(c("chr1:1-2",
"chr2:100000-100002",
"chr3:99999-100002",
"chr4:10000001-10000002"))
seqlengths(annotationsEnh) <- seqlengths(annotationsGenes) <- rep(10000002,
4)
interactions = GInteractions(annotationsEnh,annotationsGenes,
name=c("gen1","gen2","gen3","gen4"))
geneAnnotations=second(interactions)
mcols(geneAnnotations) <- mcols(interactions)
# Planned combinations
# 1) intset NULL, geneA 1 #expO: gen1
# 2) intset full, geneA 1 #expO: gen1,gen2
# 3) intset full, geneA full #expO: gen1,gen2,gen3
# 4) intset full, geneA 1&3 #expO: gen1,gen2,gen3
# 5) intset full -2 , geneA full #expO: gen1,gen3
# 6) intset 4, geneA 4 no overlap identified
# Combinations when intset does not contain info about gene, whereas
# it needs to be infered from geneAnnotations
# 7) intset full, geneA 1
# 8) intset full, geneA full
# 9) ? intset full, geneA full
################################################
####### TEST annotatewindows
test_that("annotatewindows INPUT/OUTPUT is correct in form",{
# TEST INPUT:
expect_true(class(windows)=="GRanges")
expect_true(class(geneAnnotations)=="GRanges")
expect_true(class(interactions)=="GInteractions")
# test expected input meta-data:
expect_equal(colnames(mcols(interactions)),"name")
expect_equal(colnames(mcols(geneAnnotations)),"name")
# TEST OUTPUT - QFR
# is GRanges with lenght>0
QFR <- reg2gene(windows = windows,
interactions=interactions,
geneAnnotations = geneAnnotations)
expect_is(QFR,"GInteractions")
expect_equal(names(mcols(QFR)),c("name","annotatedAs"))
# if interactions is NULL is GRanges object - works ok
QFR <- reg2gene(windows = windows,
interactions=NULL,
geneAnnotations = geneAnnotations)
expect_is(QFR,"GInteractions")
expect_equal(names(mcols(QFR)),c("name","annotatedAs"))
# if interactions have no info about gene - just geneAnnot have info
interactions2 <- interactions
mcols(interactions2) <- NULL
QFR <- reg2gene(windows = windows,
interactions=interactions2,
geneAnnotations = geneAnnotations,
annotateInteractions = TRUE)
expect_is(QFR,"GInteractions")
expect_equal(names(mcols(QFR)),c("name","annotatedAs"))
})
test_that("reg2gene arguments are correctly used",{
# 1) intset NULL, geneA 1 #expO: gen1
QFR <- reg2gene(windows = windows,
interactions = NULL,
geneAnnotations = geneAnnotations[1])
expect_equal(length(QFR),1)
expect_equal(QFR$name,"gen1")
expect_equal(granges(second(QFR)),granges(geneAnnotations[1]))
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = NULL,
geneAnnotations = geneAnnotations[1],
identified = FALSE), windows[-1])
# 2) intset full, geneA 1 #expO: gen1,gen2
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1])
expect_equal(length(QFR),2) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","enhancer"))
expect_false("gen4"%in%QFR$name)
expect_false("gen3"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1],
identified = FALSE), windows[3:4])
# 3) intset full, geneA full #expO: gen1,gen2,gen3
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations)
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene","enhancer"))
expect_false("gen4"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
identified = FALSE), windows[4])
# 4) intset full, geneA 1&3 #expO: gen1,gen2,gen3
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations[c(1,3)])
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene","enhancer"))
expect_false("gen4"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
identified = FALSE), windows[4])
# 5) intset full -2 , geneA full #expO: gen1,gen3
QFR <- reg2gene(windows,
interactions = interactions[-2],
geneAnnotations = geneAnnotations)
# Enhancer missing, but promoter failed as well
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2","gen3"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene","nearestGene"))
expect_false("gen4"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
identified = FALSE), windows[4])
# 5)a intset full -2 , geneA -2 #expO: gen1,gen3
QFR <- reg2gene(windows,
interactions = interactions[-2],
geneAnnotations = geneAnnotations[-2])
# 5a Enhancer missing, but promoter failed as well
expect_equal(length(QFR),2) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene"))
expect_false("gen4"%in%QFR$name)
expect_false("gen2"%in%QFR$name)
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = interactions[-2],
geneAnnotations = geneAnnotations[-2],
identified = FALSE), windows[c(2,4)])
# 6) intset 4, geneA 4 - no overlap identified
QFR <- reg2gene(windows,
interactions = interactions[4],
geneAnnotations = geneAnnotations[4])
expect_equal(QFR,"No overlap identified!")
# check identified=F argument
expect_equal(reg2gene(windows,
interactions = interactions[4],
geneAnnotations = geneAnnotations[4],
identified = FALSE),windows)
# test distance +/-10000000
# increase distance works well
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 10000000)
expect_equal(length(QFR),4) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen3","gen4","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","nearestGene",
"nearestGene","enhancer"))
expect_true("gen4"%in%QFR$name)
expect_equal(length(reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 10000000,identified = FALSE)),0)
# reduce distance -/+ 100
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 100)
expect_equal(length(QFR),2) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,c("promoter","enhancer"))
expect_false("gen4"%in%QFR$name)
expect_false("gen3"%in%QFR$name)
expect_equal(length(reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
distance = 100,identified = FALSE)),2)
# upstream,downstream [+/-1bp]
QFR <- reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
downstream = 1,
upstream = 1,
distance = 100)
expect_equal(length(QFR),2) # 2 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2"))
# but if distance is 1MB,then the 3rd gene should be identified as well
expect_equal( reg2gene(windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
downstream = 1, upstream = 100000,
distance = 100)$name,c("gen1","gen2",
"gen3"))
#################################################################
# ---------------------------------------------------------------
# 7) intset full, geneA 1
mcols(interactions) <- NULL
QFR <- reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1],
annotateInteractions = TRUE)
expect_equal(length(QFR),1)
expect_equal(QFR$name,"gen1")
expect_equal(granges(second(QFR)),granges(geneAnnotations[1]))
# checking identified argument as false
expect_equal(reg2gene(windows = windows,
interactions = NULL,
geneAnnotations = geneAnnotations[1],
identified = FALSE,
annotateInteractions = TRUE),
windows[-1])
# if annotateInteractions needed to be TRUE, but it is not
# defined
expect_true(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations[1])==
"ERROR! Try setting annotateInteractions = TRUE")
# 8) intset full, geneA full
QFR <- reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations,
annotateInteractions = TRUE)
expect_equal(length(QFR),3) # 3 ranges should be identified
expect_equal(QFR$name,c("gen1","gen2","gen3"))
# check annotatedAs argument
expect_equal(QFR$annotatedAs,
c("promoter","nearestGene","nearestGene"))
expect_false("gen4"%in%QFR$name)
# if annotateInteractions needed to be TRUE, but it is not
# defined
expect_true(reg2gene(windows = windows,
interactions = interactions,
geneAnnotations = geneAnnotations)==
"ERROR! Try setting annotateInteractions = TRUE")
})
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