pRoloc (version 1.12.4)

empPvalues: Estimate empirical p-values for $Chi^2$ protein correlations.

Description

Andersen et al. (2003) used a fixed $Chi^2$ threshold of 0.05 to identify organelle-specific candidates. This function computes empirical p-values by permutation the markers relative intensities and computed null $Chi^2$ values.

Usage

empPvalues(marker, corMatrix, n = 100, ...)

Arguments

marker

A numerics with markers relative intensities.

corMatrix

A matrix of nrow(corMatrix) protein relative intensities to be compares against the marker.

n

The number of iterations.

...

Additional parameters to be passed to chi2.

Value

A numeric of length nrow(corMatrix).

References

Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P. et al., Proteomic characterization of the human centrosome by protein correlation profiling. Nature 2003, 426, 570 - 574.

See Also

chi2 for $Chi^2$ calculation.

Examples

set.seed(1)
mrk <- rnorm(6, 5, 1)
prot <- rbind(matrix(rnorm(120, 5, 1), ncol = 6),
              mrk + rnorm(6))
mrk <- mrk/sum(mrk)
prot <- prot/rowSums(prot)
empPvalues(mrk, prot)