profileDistance {proteinProfiles} | R Documentation |
Compute distance between a protein group of interest and assess its significance by comparing it to the distances of randomly selected groups of proteins.
profileDistance(values, index, nSample=1000, seed) plotProfileDistance(z, ...)
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. |
List with elements:
Numeric with mean distance d_0 of profiles for the proteins of interest.
Vector of numerics with mean distances d_1 of randomly selected groups of proteins.
Numeric with p-value p.
data(ips_sample) index_28S <- grepAnnotation(annotation, pattern="^28S", column="Protein.Name") z <- profileDistance(ratios, index_28S) z$p.value plotProfileDistance(z)