test_TEtranscripts <- function() {
bamfiles <- list.files(system.file("extdata", package="atena"),
pattern="*.bam", full.names=TRUE)
TE_annot <- readRDS(file=system.file("extdata", "Top28TEs.rds",
package="atena"))
ttpar <- TEtranscriptsParam(bamfiles, teFeatures=TE_annot,
singleEnd=TRUE, ignoreStrand=TRUE,
aggregateby="repName")
ttSE <- qtex(ttpar)
checkEqualsNumeric(dim(ttSE), c(1, 2))
checkEqualsNumeric(sort(assay(ttSE), decreasing=TRUE), c(150, 123))
}
test_tt_input1 <- function() {
TE_annot <- readRDS(file=system.file("extdata", "Top28TEs.rds",
package="atena"))
checkException(TEtranscriptsParam(teFeatures=TE_annot, singleEnd=TRUE),
"An error prompts when no input BAM file is specified",
silent=TRUE)
}
test_tt_input2 <- function() {
bamfiles <- list.files(system.file("extdata", package="atena"),
pattern="*.bam", full.names=TRUE)
checkException(TEtranscriptsParam(bfl=bamfiles, singleEnd=TRUE),
"An error prompts when TE annotations are not specified",
silent=TRUE)
}
test_exon_summarization <- function() {
bamfiles <- list.files(system.file("extdata", package="atena"),
pattern="*.bam", full.names=TRUE)
TE_annot <- readRDS(file=system.file("extdata", "Top28TEs.rds",
package="atena"))
# Creating an example of gene annotations
annot_gen <- GRanges(seqnames=rep("2L",10),
ranges=IRanges(start=c(1,20,45,80,110,130,150,170,200,220),
width=c(10,20,35,10,5,15,10,25,5,20)),
strand="*",
type=rep("exon",10))
# Setting gene ids
names(annot_gen) <- paste0("gene",c(rep(1,3),rep(2,4),rep(3,3)))
annot_gen
ttpar_gen <- TEtranscriptsParam(bamfiles, teFeatures=TE_annot,
geneFeatures=annot_gen, singleEnd=TRUE,
ignoreStrand=TRUE)
checkTrue(is(features(ttpar_gen), "GRangesList"),
"Exons are summarized at the gene level in a GRangesList object")
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.