Perform a permutation correlation test on every row of a matrix — permutation_correlation

Compute a correlation value for every row of X against the vector y and n random permutations of y. If the number of possible permutations is less than the the argument n_perm then an exact test is performed instead. In both cases the function returns a data.frame of the original data with additional columns for the test statistic, empirical p-value, and FDR corrected empirical p-value.

Usage

permutation_correlation_test(X, y, n_perm = 10000, n_core = 1, ...)

Arguments

X: numeric matrix or data.frame that can be converted to a numeric matrix
y: numeric vector of values to correlate with rows of X
n_perm: integer. The desired number of permutations to sample from. Default (10,000)
n_core: integer. The number of cores to use for processing. Default (1)
...: Additional arguments to pass to `cor` function

Examples

# generate example data
X <- matrix(runif(1e3 * 10), nrow = 1e3, ncol = 10)
y <- 1:10
dimnames(X) <- list(paste("feature", 1:1e3, sep = "."), paste("sample", 1:10, sep = "."))

# correlate each row of X with 1,000 random permutations of vector y
res <- permutation_correlation_test(X, y, n_perm = 1e3, n_core = 8, method = "spearman")

head(res)
#>            sample.1  sample.2  sample.3   sample.4   sample.5   sample.6
#> feature.1 0.2662474 0.4552640 0.9013406 0.91531092 0.60306497 0.08655646
#> feature.2 0.8253921 0.4258724 0.9938062 0.57127229 0.13512341 0.17154187
#> feature.3 0.1744037 0.4352768 0.1697599 0.36899524 0.34321429 0.44868471
#> feature.4 0.6273238 0.4290254 0.7752482 0.48737756 0.47505250 0.29212738
#> feature.5 0.1609637 0.2758725 0.7283146 0.02551313 0.03749574 0.42441138
#> feature.6 0.5173081 0.2358571 0.5767007 0.34011008 0.19981703 0.80485172
#>            sample.7  sample.8   sample.9 sample.10         cor empirical.p
#> feature.1 0.7293484 0.3700858 0.92330389 0.2092298 -0.03030303       0.449
#> feature.2 0.6564562 0.7242420 0.05269735 0.7591043 -0.24848485       0.229
#> feature.3 0.1600544 0.3306400 0.43022271 0.8950066  0.33333333       0.155
#> feature.4 0.1617591 0.5021804 0.29157056 0.7514272 -0.22424242       0.265
#> feature.5 0.6551433 0.2017496 0.55512118 0.4511958  0.33333333       0.180
#> feature.6 0.5412135 0.6030285 0.72769927 0.8650728  0.69696970       0.017
#>                 FDR
#> feature.1 0.4852632
#> feature.2 0.4646465
#> feature.3 0.4517045
#> feature.4 0.4766187
#> feature.5 0.4556962
#> feature.6 0.4146341