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context("tximeta")
test_that("tximeta works as expected", {
testthat::skip("The json file contains an invalid character, skipping for now")
dir <- system.file("extdata/salmon_dm", package="tximportData")
files <- file.path(dir, "SRR1197474", "quant.sf")
coldata <- data.frame(files, names="SRR1197474", condition="A", stringsAsFactors=FALSE)
indexDir <- file.path(dir, "Dm.BDGP6.22.98_salmon-0.14.1")
fastaFTP <- c("ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.22.cdna.all.fa.gz",
"ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz")
gtfPath <- file.path(dir,"Drosophila_melanogaster.BDGP6.22.98.gtf.gz")
makeLinkedTxome(indexDir=indexDir, source="LocalEnsembl", organism="Drosophila melanogaster",
release="98", genome="BDGP6.22", fasta=fastaFTP, gtf=gtfPath, write=FALSE)
# TODO why not throwing warnings on Bioc
#expect_warning({se <- tximeta(coldata)}, "annotation is missing")
se <- tximeta(coldata)
# check adding IDs
library(org.Dm.eg.db)
se <- addIds(se, column="SYMBOL")
# check adding IDs from TxDb/EnsDb (commented out due to Ahub/EnsDb issue)
# se <- addIds(se, column="SYMBOL", fromDb=TRUE)
# check adding CDS
library(SummarizedExperiment)
se2 <- addCDS(se)
# check adding exons
se <- addExons(se)
# check adding CDS on exons
se <- addCDS(se)
# check summarize to gene
gse <- summarizeToGene(se)
expect_error(addExons(gse), "transcript-level")
# check adding IDs
library(org.Dm.eg.db)
gse <- addIds(gse, "REFSEQ", gene=TRUE)
# check retrieving the database
edb <- retrieveDb(se)
# check retrieving the cDNA sequence
if (FALSE) {
# this requires access to Ensembl ftp
cdna <- retrieveCDNA(se)
}
# just a vector of file paths is ok...
# TODO why not throwing warnings on Bioc
#expect_warning({se <- tximeta(files)})
se <- tximeta(files)
# check error on txOut=FALSE
expect_error({se <- tximeta(coldata, txOut=FALSE)},
"transcript-level output")
# check skipping metadata, appropriate warnings
se <- tximeta(coldata, skipMeta=TRUE)
expect_error({summarizeToGene(se)}, "transcriptome metadata")
expect_error({addIds(se)}, "transcriptome metadata")
# check customMetaInfo
se <- tximeta(coldata, customMetaInfo="aux_info/meta_info.json")
expect_error(tximeta(coldata, customMetaInfo="foobar.json"),
"metadata files are missing")
# check make DGEList
library(edgeR)
y <- makeDGEList(se)
})
test_that("tximeta can import GENCODE and Ensembl", {
if (FALSE) {
### GENCODE ###
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
files <- file.path(dir,"salmon", samples$run, "quant.sf.gz")
coldata <- data.frame(files, names=paste0("sample",1:6))
# with AnnotationHub (default)
se <- tximeta(coldata)
gse <- summarizeToGene(se)
# check adding IDs from TxDb/EnsDb
se <- addIds(se, column="TXTYPE", fromDb=TRUE)
# without AnnotationHub
se <- tximeta(coldata, useHub=FALSE)
### Ensembl ###
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
files <- file.path(dir,"salmon_gibbs", samples$run, "quant.sf.gz")
coldata <- data.frame(files, names=paste0("sample",1:6))
# with AnnotationHub (default)
se <- tximeta(coldata, dropInfReps=TRUE, useHub=TRUE)
# without AnnotationHub
se <- tximeta(coldata, dropInfReps=TRUE, useHub=FALSE)
gse <- summarizeToGene(se)
# test the mark duplicate code
dir <- system.file("extdata", package="macrophage")
samples <- list.files(file.path(dir, "quants"))[1:3]
files <- file.path(dir,"quants", samples, "quant.sf.gz")
coldata <- data.frame(files, names=paste0("sample",1:3))
se <- tximeta(coldata, dropInfReps=TRUE, markDuplicateTxps=TRUE)
gse <- summarizeToGene(se)
}
})
test_that("tximeta can import inferential replicates", {
# don't want to rely on internet connection for tests...
if (FALSE) {
library(SummarizedExperiment)
# check the GEUVADIS samples with Salmon Gibbs samples
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
files <- file.path(dir,"salmon_gibbs", samples$run, "quant.sf.gz")
coldata <- data.frame(files, names=paste0("sample",1:6))
se <- tximeta(coldata)
expect_true("infRep1" %in% assayNames(se))
se2 <- tximeta(coldata, varReduce=TRUE)
expect_true("variance" %in% assayNames(se2))
gse <- summarizeToGene(se)
expect_true("infRep1" %in% assayNames(gse))
gse <- summarizeToGene(se, varReduce=TRUE)
expect_true("variance" %in% assayNames(gse))
# check the macrophage dataset with Salmon Gibbs samples
dir <- system.file("extdata", package="macrophage")
coldata <- read.csv(file.path(dir, "coldata.csv"))
coldata$files <- file.path(dir, "quants", coldata$names, "quant.sf.gz")
coldata <- coldata[1:2,]
se <- tximeta(coldata)
se <- tximeta(coldata, skipSeqinfo=TRUE)
}
})
test_that("tximeta can import alevin", {
testthat::skip("There is no alevin file present, skip")
dir <- system.file("extdata", package="tximportData")
samps <- list.files(file.path(dir, "alevin"))
files <- file.path(dir,"alevin",samps[1],"alevin/quants_mat.gz")
file.exists(files)
coldata <- data.frame(files, names="neurons")
#se <- tximeta(coldata, type="alevin")
se <- tximeta(coldata, type="alevin", skipMeta=TRUE)
})
test_that("tximeta can import refseq", {
if (FALSE) {
dir <- system.file("extdata", package="tximportData")
files <- file.path(dir,"refseq/ERR188021/quant.sf.gz")
file.exists(files)
coldata <- data.frame(files, names="A")
# here the important test is if we can pull down seqinfo
# (sequence names and lengths) from RefSeq FTP site
se <- tximeta(coldata)
seqinfo(se)
}
})
test_that("tximeta can import kallisto", {
if (requireNamespace(package="rhdf5", quietly=TRUE)) {
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
files <- file.path(dir,"kallisto", samples$run, "abundance.tsv.gz")
coldata <- data.frame(files, names=paste0("sample",1:6))
se <- tximeta(coldata, type="kallisto", txOut=TRUE)
# inferential replicates as well
library(SummarizedExperiment)
files <- file.path(dir,"kallisto_boot", samples$run, "abundance.h5")
coldata <- data.frame(files, names=paste0("sample",1:6))
se <- tximeta(coldata, type="kallisto", txOut=TRUE)
expect_true("infRep1" %in% assayNames(se))
se <- tximeta(coldata, type="kallisto", txOut=TRUE, varReduce=TRUE)
expect_true("variance" %in% assayNames(se))
}
})
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