nearestProts: Identifies proteins with profiles similar to that of a...

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Identifies proteins with profiles similar to that of a specified protein.

Description

Uses a distance matrix to identify proteins with profiles nearest to that of a specified protein; can be used to identify proteins with similar subcellular locations.

Usage

nearestProts(protName, n.nearest = 5, distProts, protNames, profile)

Arguments

protName	name of protein to which distances are to be computed
n.nearest	number of nearest proteins to list
distProts	distance matrix created by, for example, using the 'dist' function in R
protNames	list of all proteins in a dataset
profile	data frame of profiles for proteins

Value

List of the proteins in data set with profiles closest to that of specified protein (protName)

Examples

data(protNSA_test)
distUse <- dist(protNSA_test[,seq_len(9)], method='euclidean')
protsUse <- names(protNSA_test)
nearestProts(protName='CTSD', n.nearest=10,  distProts=distUse,
  protNames=protsUse, profile=protNSA_test[,seq_len(9)])

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.