data-raw/DATASET.R

In bambu: Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

## code to prepare `sysdata.rda` dataset goes here

a <- 500

data1 <- data.frame(
    tx_id = c(1, 2, 3, 1, 2, 1, 2, 3),
    read_class_id = c(1, 2, 3, rep(4, 2), rep(5, 3)),
    nobs = c(0, 0, 0, rep(10, 2), rep(a, 3)),
    gene_id = 1
)

data2 <- data.frame(
    tx_id = c(1, 2, 1, 2, 3),
    read_class_id = c(rep(4, 2), rep(5, 3)),
    nobs = c(rep(10, 2), rep(a, 3)),
    gene_id = 2
)

data3 <- data.frame(
    tx_id = c(1, 2),
    read_class_id = c(1, 2),
    nobs = c(5, 10),
    gene_id = 3
)

data4 <- data.frame(
    tx_id = c(1, 2, 3, 1, 2, 1, 2, 3),
    read_class_id = c(1, 2, 3, rep(4, 2), rep(5, 3)),
    nobs = c(100, 5, 500, rep(20, 2), rep(5, 3)),
    gene_id = 4
)

data5 <- data.frame(
    tx_id = c(1:6, 2, 3, 1, 2, 5, 1, 2, 3, 5, 1:5),
    read_class_id = c(1:6, rep(7, 2), rep(8, 3), rep(9, 4), rep(10, 5)),
    nobs = c(2, 0, 1, 0, 0, 1, rep(2, 2), rep(282, 3), rep(64, 4), rep(5, 5)),
    gene_id = 5
)



estOutput_woBC <- lapply(1:5, function(s) {
    est <- bambu.quantDT(readClassDt = get(paste0("data", s)), emParameters = list(bias = FALSE))
})

estOutput_wBC <- lapply(1:5, function(s) {
    est <- bambu.quantDT(readClassDt = get(paste0("data", s)))
})



## expected output for test isore

seReadClass1 <- readRDS(system.file("extdata", "seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds", package = "bambu"))
extendedAnnotations <- readRDS(system.file("extdata", "extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds", package = "bambu"))
gr <- readRDS(system.file("extdata", "annotationGranges_txdbGrch38_91_chr9_1_1000000.rds", package = "bambu"))


seWithDistExpected <- isore.estimateDistanceToAnnotations(
    seReadClass = seReadClass1,
    annotationGrangesList = extendedAnnotations,
    min.exonDistance = 35
)


## expected seGeneOutput

se <- readRDS(system.file("extdata", "seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds", package = "bambu"))
seExtended <- readRDS(system.file("extdata", "seOutputExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds", package = "bambu"))
seCombined <- readRDS(system.file("extdata", "seOutputCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds", package = "bambu"))
seCombinedExtended <- readRDS(system.file("extdata", "seOutputCombinedExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds", package = "bambu"))


seGeneExpected <- transcriptToGeneExpression(se)
seExtendedGeneExpected <- transcriptToGeneExpression(seExtended)
seCombinedGeneExpected <- transcriptToGeneExpression(seCombined)
seCombinedExtendedGeneExpected <- transcriptToGeneExpression(seCombinedExtended)


set.seed(1234)
seqlevelsStyle(gr) <- "UCSC"
seUCSCExpected <- bambu(reads = test.bam, annotations = gr, genomeSequence = fa.file, extendAnnotations = FALSE)




usethis::use_data(data1, data2, data3, data4, data5,
    estOutput_woBC,
    estOutput_wBC,
    standardJunctionModels_temp,
    seWithDistExpected,
    seGeneExpected, seExtendedGeneExpected,
    seCombinedGeneExpected, seCombinedExtendedGeneExpected,
    seUCSCExpected,
    internal = TRUE, overwrite = TRUE
)