# test_col1a1.R
#------------------------------------------------------------------------------------------------------------------------
library(TrenaGene)
library(RUnit)
library(TrenaGeneSkinData)
#------------------------------------------------------------------------------------------------------------------------
runTests <- function()
{
test_basic()
test_withExpressionData()
test_getEnhancers()
test_getEncodeDHS()
test_getChipSeq()
} # runTests
#------------------------------------------------------------------------------------------------------------------------
test_basic <- function()
{
printf("--- test_basic")
col1a1 <- TrenaGene("COL1A1", "hg38")
checkTrue("TrenaGene" %in% is(col1a1))
tbl <- getTranscriptsTable(col1a1)
checkEquals(dim(tbl), c(14, 30))
gene.min <- subset(tbl, moleculetype=="gene")$start
gene.max <- subset(tbl, moleculetype=="gene")$endpos
checkTrue(min(tbl$start) == gene.min)
checkTrue(max(tbl$endpos) == gene.max)
transcript.lengths <- sort(with(tbl, 1 + endpos-start))
checkEquals(transcript.lengths, c(517, 574, 616, 867, 893, 903, 948, 1279, 2116, 2183, 2355, 3150, 18344, 18344))
checkEquals(getExpressionMatrixNames(col1a1), list())
} # test_basic
#------------------------------------------------------------------------------------------------------------------------
test_withExpressionData <- function()
{
printf("--- test_withExpressionData")
dataDirectory <- system.file(package="TrenaGeneSkinData", "extdata")
checkTrue(file.exists(dataDirectory))
col1a1 <- TrenaGene("COL1A1", "hg38", expressionDataDirectory=dataDirectory)
checkTrue("TrenaGene" %in% is(col1a1))
matrix.names <- getExpressionMatrixNames(col1a1)
checkTrue(length(matrix.names) >= 4)
checkTrue("mtx.protectedAndExposed" %in% matrix.names)
} # test_withExpressionData
#------------------------------------------------------------------------------------------------------------------------
test_getEnhancers <- function()
{
printf("--- test_getEnhancers")
dataDirectory <- system.file(package="TrenaGeneSkinData", "extdata")
col1a1 <- TrenaGene("COL1A1", "hg38", expressionDataDirectory=dataDirectory)
checkTrue("TrenaGene" %in% is(col1a1))
tbl.enhancers <- getEnhancers(col1a1)
checkEquals(dim(tbl.enhancers), c(32, 6))
checkEquals(colnames(tbl.enhancers), c("chrom", "start", "end", "type", "combinedScore", "geneSymbol"))
} # test_getEnhancers
#------------------------------------------------------------------------------------------------------------------------
test_getEncodeDHS <- function()
{
printf("--- test_getEncodeDHS")
dataDirectory <- system.file(package="TrenaGeneSkinData", "extdata")
col1a1 <- TrenaGene("COL1A1", "hg38", expressionDataDirectory=dataDirectory)
checkTrue("TrenaGene" %in% is(col1a1))
tbl.dhs <- getEncodeDHS(col1a1)
checkTrue(nrow(tbl.dhs) > 2000)
checkEquals(colnames(tbl.dhs), c("chrom", "chromStart", "chromEnd", "count", "score"))
} # test_getEncodeDHS
#------------------------------------------------------------------------------------------------------------------------
test_getChipSeq <- function()
{
printf("--- test_getChipSeq")
dataDirectory <- system.file(package="TrenaGeneSkinData", "extdata")
col1a1 <- TrenaGene("COL1A1", "hg38", expressionDataDirectory=dataDirectory)
checkTrue("TrenaGene" %in% is(col1a1))
tbl.enhancers <- getEnhancers(col1a1)
tbl.strong <- subset(tbl.enhancers, combinedScore > 500)
chrom <- tbl.strong$chrom[1]
loc.min <- tbl.strong$start[1]
loc.max <- tbl.strong$end[1]
tbl.chipSeq <- getChipSeq(col1a1, "chr17", 50200750, 50201000)
checkTrue(nrow(tbl.chipSeq) > 30)
checkEquals(colnames(tbl.chipSeq),
c("chr", "start", "end", "tf", "name", "peakStart", "peakEnd"))
} # test_getChipSeq
#------------------------------------------------------------------------------------------------------------------------
if(!interactive()) runTests()
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