TileReadSignalHelper {TileShuffle}R Documentation

TileReadSignalHelper

Description

Reads a TAS-created signal.txt file.

Usage

TileReadSignalHelper(filename, minhits, verbose)

Arguments

filename Filename of human-readable signal.txt file (as a character) created by the Tiling Array Software (TAS).
minhits Minimal number of hits in BPMAP entry to be considered for the further analysis. Due to historical reasons there are several entries in the BPMAP file with only around thousand probes assigned that might overlap with the larger entries or with entries on other tiling arrays.
verbose Indicates whether information on progress are printed.

Details

Reads a human-readable signal.txt file created by the Tiling Array Software (TAS) from Affymetrix. The signal files comprise information on the genomic map entry (e.g. chromosome name), probe center positions and probe intensities. The intensities are assumed to be in log2 scale. The method generates a list for each genomic map entry containing the center position and intensity of the corresponding probes.

Value

Returns a list for each genomic map entry containing the center position and intensity of all corresponding probes.


[Package TileShuffle version 0.1.0 Index]