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

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/chi2.R

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

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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 <lg390@cam.ac.uk>

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

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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)

pRoloc documentation built on Nov. 8, 2020, 6:26 p.m.