inst/unitTests/test_getSGVariantCounts.R

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

test_getSGVariantCounts <- function()
{

    sgvc_from_sgfc <- getSGVariantCounts(sgv_pred, feature_counts = sgfc_pred)
    SGSeq:::checkIdenticalSummarizedExperiment(sgvc_pred, sgvc_from_sgfc)

    path <- system.file("extdata", package = "SGSeq")
    si$file_bam <- file.path(path, "bams", si$file_bam)
    sgvc_from_bam <- getSGVariantCounts(sgv_pred, sample_info = si)
    SGSeq:::checkIdenticalSummarizedExperiment(
        sgvc_pred_from_bam, sgvc_from_bam)

    counts(sgvc_from_bam, option = "variant5pOr3p") <- NULL
    SGSeq:::checkIdenticalSummarizedExperiment(sgvc_from_sgfc, sgvc_from_bam)

}