filterMinMarkers: Removes class/annotation information from a matrix of...

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

Removes class/annotation information from a matrix of candidate markers that appear in the fData.

Description

Removes annotation information that contain less that a certain number/percentage of proteins

Usage

filterMinMarkers(object, n = 10, p, fcol = "GOAnnotations", verbose = TRUE)

Arguments

object	An instance of class MSnSet.
n	Minimum number of proteins allowed per column. Default is 10.
p	Minimum percentage of proteins per column.
fcol	The name of the matrix of marker information. Default is GOAnnotations.
verbose	Number of marker candidates retained after filtering.

Value

An updated MSnSet.

Author(s)

Lisa M Breckels

Examples

library(pRolocdata)
data(dunkley2006)
xx <- dunkley2006
## create a matrix of markers
xx <- mrkVecToMat(xx, vfcol = "markers", mfcol = "Markers")
## Remove marker classes with less than 15 members, from matrix of markers
xx <- filterMinMarkers(xx, n = 15, fcol = "Markers")
## Remove marker classes with more than 50 members, from matrix of markers
xx <- filterMaxMarkers(xx, p = .2, fcol = "Markers")

lgatto/pRoloc documentation built on June 14, 2025, 7:56 p.m.