Compute columnwise ranks of matrix

Computes columnwise rank of matrix. Can be sparse. Tries to call optimized functions from Rfast or matrixStats.

Usage

colranks(
  X,
  sparse = NULL,
  signed = FALSE,
  keep.zero = FALSE,
  ties.method = "average"
)

Arguments

X: Input matrix
sparse: Logical indicating to use sparse methods
signed: Logical indicating using signed ranks
keep.zero: Logical indicating whether to keep zero as ranked zero
ties.method: Character Choice of ties.method

Value

Matrix of columnwise ranks with same dimensions as input.

Examples

# Create example matrix
set.seed(123)
X <- matrix(rnorm(100), nrow = 10, ncol = 10)
rownames(X) <- paste0("Gene", 1:10)
colnames(X) <- paste0("Sample", 1:10)

# Compute column ranks
ranks <- colranks(X)
print(ranks[1:5, 1:5])
#>       Sample1 Sample2 Sample3 Sample4 Sample5
#> Gene1       3       9       3       5       3
#> Gene2       5       5       7       3       6
#> Gene3       9       6       4      10       1
#> Gene4       6       4       5       9      10
#> Gene5       7       2       6       8       9

# Compute signed ranks
signed_ranks <- colranks(X, signed = TRUE)
print(signed_ranks[1:5, 1:5])
#>       Sample1 Sample2 Sample3 Sample4 Sample5
#> Gene1      -6       8      -7       5      -5
#> Gene2      -3       2      -2      -2      -2
#> Gene3       9       3      -6      10      -9
#> Gene4       1       1      -4       9      10
#> Gene5       2      -6      -3       8       8