proteinProfiles (version 1.12.1)

profileDistance: profileDistance

Description

Compute distance between a protein group of interest and assess its significance by comparing it to the distances of randomly selected groups of proteins.

Usage

profileDistance(values, index, nSample=1000, seed)
plotProfileDistance(z, ...)

Arguments

values

Numeric matrix containing the protein data to analyze.

index

Protein identifiers for the protein group of interest in the data set ‘values’, as returned from ‘grepAnnotation’ or an equivalent function.

nSample

Integer specifying the number of randomly selected groups of proteins with the same number of elements as specified by ‘index’, serving as a reference for the significance assessment (default: 1000).

seed

Random seed, relevant for the permutation step. For details, see the ‘seed’ function.

z

Return object from ‘profileDistance.’

...

Optional arguments passed to the ‘plot’ function.

Value

List with elements:

d0

Numeric with mean distance $d_0$ of profiles for the proteins of interest.

d1

Vector of numerics with mean distances $d_1$ of randomly selected groups of proteins.

p

Numeric with p-value $p$.

Examples

data(ips_sample)

index_28S <- grepAnnotation(annotation, pattern="^28S",
column="Protein.Name")

z <- profileDistance(ratios, index_28S)

z$p.value

plotProfileDistance(z)