Nothing
# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text.
# OICR makes no representations whatsoever as to the SOFTWARE contained herein. It is experimental in nature and is provided WITHOUT
# WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
# OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
# By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
# nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
# If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
# credit be given to OICR scientists, as scientifically appropriate.
context("determine.input")
if (check.binary("tabix", verbose = TRUE)) {
test_that("check that input format is correctly identified", {
regions <- get.example.regions()
region.a.bed.df1 <- index2bed(regions$a)
region.a.bed.df2 <- index2bed(regions$a)
colnames(region.a.bed.df2) <- c("a","b","c")
region.a.index.df1 <- data.frame(index=regions$a, score = 1:length(regions$a), stringsAsFactors=F)
region.a.index.df2 <- data.frame(matrix(ncol=3,nrow=length(regions$a)), row.names=regions$a, stringsAsFactors=F)
a <- bedr(engine = "bedtools", input = list(i = regions$a), method = "sort", params = "");
b <- bedr(engine = "bedtools", input = list(i = regions$b), method = "sort", params = "");
# index
expect_equal(determine.input(a, verbose = F), 0);
# bed
expect_equal(determine.input(region.a.bed.df1, verbose = F), 1) # df with correct names
expect_equal(determine.input(as.matrix(region.a.bed.df1), verbose = F), 1) # matrix with correct names
expect_equal(determine.input(region.a.bed.df2, verbose = F), 1) # df with incorrect names
# column index
expect_equal(determine.input(region.a.index.df1, verbose = F), 2);
# row index
expect_equal(determine.input(region.a.index.df2, verbose = F), 3);
expect_equal(determine.input(as.matrix(region.a.bed.df2), verbose = F), 4) # matrix with incorrect names fails due to string conversion
expect_equal(determine.input(as.matrix(regions$a), verbose = F), 4); # need to be more explicit
expect_equal(determine.input(NA, verbose = F), 4) # a vector but it doesn't look like an index
})
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.