fisherTests: Compute Fisher-tests for a BSseq object
In bsseq: Analyze, manage and store bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also Examples

A function to compute Fisher-tests for an object of class BSseq.

1 2	fisherTests(BSseq, group1, group2, lookup = NULL, returnLookup = TRUE, mc.cores = 1, verbose = TRUE)

`BSseq`	An object of class `BSseq`.
`group1`	A vector of sample names or indexes for the ‘treatment’ group.
`group2`	A vector of sample names or indexes for the ‘control’ group.
`lookup`	A ‘lookup’ object, see details.
`returnLookup`	Should a ‘lookup’ object be returned, see details.
`mc.cores`	The number of cores used. Note that setting `mc.cores` to a value greater than 1 is not supported on MS Windows, see the help page for `mclapply`.
`verbose`	Should the function be verbose.

This function computes row-wise Fisher's exact tests. It uses an internal lookup table so rows which forms equivalent 2x2 tables are group together and only a single test is computed. If returnLookup is TRUE the return object contains the lookup table which may be feed to another call to the function using the lookup argument.

If group1, group2 designates more than 1 sample, the samples are added together before testing.

This function can use multiple cores on the same computer.

This test cannot model biological variability.

if returnLookup is TRUE, a list with components results and lookup, otherwise just the results component. The results (component) is a matrix with the same number of rows as the BSseq argument and 2 columns p.value (the unadjusted p-values) and log2OR (log2 transformation of the odds ratio).

Kasper Daniel Hansen khansen@jhsph.edu

fisher.test for information about Fisher's test. mclapply for the mc.cores argument.

M <- matrix(1:9, 3,3)
colnames(M) <- c("A1", "A2", "A3")
BStest <- BSseq(pos = 1:3, chr = c("chr1", "chr2", "chr1"),
                M = M, Cov = M + 2)
results <- fisherTests(BStest, group1 = "A1", group2 = "A2",
                       returnLookup = TRUE)
results

#-------------------------------------------------------------------------------
# An example using a HDF5Array-backed BSseq object
#
library(HDF5Array)
# See ?SummarizedExperiment::saveHDF5SummarizedExperiment for details
hdf5_BStest <- saveHDF5SummarizedExperiment(x = BStest,
                                            dir = tempfile())
results <- fisherTests(hdf5_BStest,
                       group1 = "A1",
                       group2 = "A2",
                       returnLookup = TRUE)
results