map2design: Update a track coordinates to match a distinct CGH design

In cghRA: Array CGH Data Analysis and Visualization

Description

Remapping a track.table object storing genomic segments to a specific CGH design consists of two steps :

• The production of a map, which defines the coordinates of each segment by the indexes of the first and last CGH probes included in it (map2design).

• The update of the genomic coordinates of the original track, using the map and the design (applyMap).

Usage

  map2design(track, design, minProbes = 1, quiet = FALSE, warn = TRUE)
  applyMap(track, map, design)

Arguments

track	A track.table-inheriting object, storing one row for each genomic segment of interest in a CGH-like experiment.
design	A track.table-inheriting object (preferably a cghRA.design object), storing one row for each probe in the design data is to be remapped on.
minProbes	Single integer value, the amount of probes a segment in track must cover to be retained.
quiet	Single logical value, whether to print diagnostic messages or not.
map	An integer matrix defining the mapping of track to design, as produced by map2design.
warn	Single logical value, to be passed to the check method of the newly created segmentMap object.

Value

map2design returns an integer matrix with 3 columns and row names. Columns "start" and "end" define the coordinates of a segment as probe indexes in design, and column "count" allow to group segments with the same remapped coordinates. Row names correspond to the index range of the corresponding segments in the original track.

applyMap returns a copy of track, in which start and end coordinates have been updated to match coordinates of probes in design. Segments that do not overlap at least minProbes probe in design are excluded.

Author(s)

Sylvain Mareschal

See Also

cnvScore

cghRA documentation built on May 2, 2019, 3:34 a.m.