# correlation: Correlation In acidgenomics/basejump: Base Functions for Bioinformatics

Correlation

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28``` ```correlation(x, y, ...) ## S4 method for signature 'numeric,numeric' correlation(x, y, method = c("pearson", "kendall", "spearman")) ## S4 method for signature 'matrix,missingOrNULL' correlation(x, y = NULL, method = c("pearson", "kendall", "spearman")) ## S4 method for signature 'matrix,matrix' correlation(x, y, method = c("pearson", "kendall", "spearman")) ## S4 method for signature 'Matrix,missingOrNULL' correlation(x, y = NULL, method = c("pearson", "kendall", "spearman")) ## S4 method for signature 'Matrix,Matrix' correlation(x, y, method = c("pearson", "kendall", "spearman")) ## S4 method for signature 'SummarizedExperiment,missingOrNULL' correlation( x, y = NULL, i = 1L, j = NULL, method = c("pearson", "kendall", "spearman") ) ## S4 method for signature 'SummarizedExperiment,SummarizedExperiment' correlation(x, y, i = 1L, method = c("pearson", "kendall", "spearman")) ```

## Arguments

 `x` Object. `y` Object. `method` a character string indicating which correlation coefficient (or covariance) is to be computed. One of `"pearson"` (default), `"kendall"`, or `"spearman"`: can be abbreviated. `i` `integer(1)` or `character(1)`. For `SummarizedExperiment`, primary assay. `j` `integer(1)`, `character(1)`, or `NULL`. For `SummarizedExperiment`, optional secondary assay. If `NULL`, calculates correlation matrix only on the primary assay. `...` Additional arguments.

## Value

`numeric(1)` or `matrix`.

## Note

Updated 2020-01-20.

• `stats::cor()`.

• `stats::cor.test()`.

• `stats::sd()`.

• `S4Vectors::cor()`.

• https://stats.stackexchange.com/questions/24980

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32``` ```data(correlation, package = "acidtest") list <- correlation ## vector ==== x <- list[["vector_x"]] y <- list[["vector_y"]] head(x) head(y) correlation(x = x, y = y) ## matrix ==== x <- list[["matrix_x"]] y <- list[["matrix_y"]] head(x) head(y) stats::cor(x) correlation(x) stats::cor(x = c(x), y = c(y)) correlation(x = x, y = y) ## SummarizedExperiment ==== x <- list[["SummarizedExperiment_x"]] y <- list[["SummarizedExperiment_y"]] correlation(x = x, i = 1L) correlation(x = x, i = 1L, j = 2L) correlation(x = x, y = y) ```

acidgenomics/basejump documentation built on Aug. 15, 2020, 10:21 a.m.