Description Usage Arguments Details Examples
The Row-Column-Exclusivity or Co-mutation test measures the likelihood of
seeing the number of mutually exclusive or co-mutation events between sets of
genes of size k
given the number of mutations per gene and per sample.
By accounting for the number of mutations per sample, this test is more
sensitive than using a one-sided Fisher's exact test (for when k=2
) or
CoMEt (for when k>2
).
1 2 3 |
dat |
tibble with mutation information |
sample_col |
column of samples names (quoted) |
mutgene_col |
column of genes that are mutated (quoted) |
k |
size of gene sets to consider (default is 2) |
which_test |
test for mutual exclusivity ( |
seed_genes |
a vector of gene(s) that must be in the gene set to be tested (optional) |
N_perms |
number of permutation matrices to use (default is 10,000) |
min_mut_events |
minimum number of real mutual exclusive events required to consider the gene set (default is 2) |
min_times_mut |
minimum number of times a gene must be mutated in all samples to be considered for the gene sets (default is 5) |
This test cannot be calculated exactly for most use cases because there is no closed formula and a very large number of possible matrices to consider. Thus, the probabilities are calculated empirically from a sufficiently large number of samples of possible matrices.
1 2 3 | library(wext)
set.seed(0)
rc_test(simple_dataset, sample_name, mutated_gene, k = 2, N_perms = 2)
|
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