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

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

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).

Author(s)

Laurent Gatto <[e-mail]>

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)

lgatto/pRoloc documentation built on Oct. 23, 2024, 12:51 a.m.