/usr/lib/R/site-library/SummarizedExperiment/unitTests/test_makeSummarizedExperimentFromDataFrame.R is in r-bioc-summarizedexperiment 1.8.0-1.
This file is owned by root:root, with mode 0o644.
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rowNames <- paste0("GENE", letters[5:1])
range_info <- list(chr="chr2", start = 11:15, end = 12:16,
strand = c("+", "-", "+", "*", "."))
expr_info <- list(expr0 = 3:7, expr1 = 8:12, expr2 = 12:16)
df <- as.data.frame(c(range_info, expr_info), row.names = rowNames)
DF <- DataFrame(c(range_info, expr_info), row.names = rowNames)
test_makeSummarizedExperimentFromDataFrame <- function()
{
validObject(makeSummarizedExperimentFromDataFrame(df))
validObject(makeSummarizedExperimentFromDataFrame(DF))
rangesA <- GRanges(as.data.frame(range_info, row.names = rowNames))
rangesB <- rowRanges(makeSummarizedExperimentFromDataFrame(df))
# Check rowRanges to be identical
checkIdentical(rangesA, rangesB)
# Check assay matrix and expr_info matrix are identical
checkIdentical(assay(makeSummarizedExperimentFromDataFrame(df)),
as.matrix(as.data.frame(expr_info, row.names = rowNames)))
checkIdentical(assay(makeSummarizedExperimentFromDataFrame(DF)),
as.matrix(as.data.frame(expr_info, row.names = rowNames)))
checkEquals(makeSummarizedExperimentFromDataFrame(df),
makeSummarizedExperimentFromDataFrame(DF))
checkException(
makeSummarizedExperimentFromDataFrame(
cbind(df, expr3 = letters[seq_len(nrow(df))])))
checkException(
makeSummarizedExperimentFromDataFrame(
cbind(DF, DataFrame(expr3 = letters[seq_len(nrow(df))]))))
checkIdentical(nrow(df),
length(rowRanges(
makeSummarizedExperimentFromDataFrame(df))))
checkIdentical(nrow(DF),
length(rowRanges(
makeSummarizedExperimentFromDataFrame(DF))))
checkIdentical(colnames(makeSummarizedExperimentFromDataFrame(df)),
names(expr_info))
checkIdentical(rownames(makeSummarizedExperimentFromDataFrame(df)),
rowNames)
checkIdentical(colnames(makeSummarizedExperimentFromDataFrame(DF)),
names(expr_info))
checkIdentical(rownames(makeSummarizedExperimentFromDataFrame(DF)),
rowNames)
}
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