LOMAR (version 0.5.0)

point_sets_from_locs: point_sets_from_locs

Description

Extracts list of point sets from a data frame of single molecule localization coordinates. By default, uses point set membership indicated in the site column.

Usage

point_sets_from_locs(
  locs = NULL,
  channels = NULL,
  min.cardinality = NULL,
  max.cardinality = NULL,
  crop.size = NULL,
  keep.locprec = TRUE,
  sample.size = NULL,
  ignore.site = FALSE,
  cluster.points = FALSE,
  eps = NULL,
  minPts = NULL
)

Value

a list of matrices with columns x,y,z, optionally locprec and name set to the value of the site column (if applicable).

Arguments

locs,

a data frame with columns x[nm], y[nm], z[nm] and optionally site[numbers], locprec[nm] and locprecz[nm], other columns are ignored.

channels

vector of integers indicating which channel(s) of a multicolour experiment to extract point sets from.

min.cardinality

filter out point sets with less than the specified number of points.

max.cardinality

filter out point sets with more than the specified number of points.

crop.size

remove points from a set if they are further away than the specified distance from the center of the set.

keep.locprec

logical (default:TRUE). Whether to keep locprec information for each point.

sample.size

returns this number of randomly selected point sets. Selects the point sets after applying eventual filtering.

ignore.site

logical (default: FALSE), set to TRUE if point set membership is not present or needed.

cluster.points

logical (default: FALSE), whether to cluster the points using DBSCAN (only if ignore.site is also TRUE).

eps

DBSCAN parameter, size of the epsilon neighbourhood

minPts

DBSCAN parameter, number of minimum points in the eps region

Examples

data.file <- system.file("test_data", "simulated_NUP107_data.csv", package = "LOMAR",
 mustWork = TRUE)
locs <- locs_from_csv(file = data.file, locprec.filter = 20)
point.sets <- point_sets_from_locs(locs, keep.locprec = TRUE, min.cardinality = 15)