# test_seurat_conversion.R
# Copyright (C) 2019 Rahul Dhodapkar
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
context("ConvertToSeurat")
library(melange)
dname = "../testdata/rsem"
cells <- c("cell1", "cell2", "cell3")
rsem.files <- paste(cells, "rsem_quant.genes.results", sep=".")
rsem.files.fullpath <- paste(dname, rsem.files, sep="/")
rsem.assay.TPM <- SeuratAssayFromMelange(LoadRSEM(
cells = cells,
rsem.filenames = rsem.files.fullpath,
quantitation.method = 'TPM'
))
rsem.assay.count <- SeuratAssayFromMelange(LoadRSEM(
cells = cells,
rsem.filenames = rsem.files.fullpath,
quantitation.method = 'count'
))
test_that("RSEM files to Seurat Assay from Melange", {
expect_is(rsem.assay.count, "Assay")
expect_is(rsem.assay.TPM, "Assay")
})
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