| TileReadSignal {TileShuffle} | R Documentation |
Reads tiling array data from an Affymetrix BPMAP file and a TAS-created signal.txt file.
TileReadSignal(signal.filename, bpmap.filename, minhits=8000,
group="Hs", gc=TRUE, matchscore=FALSE, verbose=FALSE)
signal.filename |
Filename of human-readable signal.txt file
(as a character) created by the Tiling Array Software (TAS). |
bpmap.filename |
Filename of Affymetrix binary probe mapping (BPMAP)
file (as a character), which is a binary file containing
information on the location of each probe in the reference sequence.
Moreover, it stores the probe sequences that are necessary to
calculate the GC content. |
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. In case of Affy tiling array 1.0R, a value of 8000 is recommended. |
group |
A group name as the organism abbreviation in order to consider only these entries in the BPMAP file and hence disregard entries such as TIGR, Affymetrix, or bacterial controls. |
gc |
Indicates whether GC content of probe sequences will be calculated. It is defined as fraction of both Gs and Cs in the probe sequence. |
matchscore |
Indicates whether match score will be read. The match score is defined as number of perfect matches of the probe sequence per megabase of the genomic sequence. This information needs to be set accordingly in the BPMAP file. Otherwise, all probes contain only the default value. |
verbose |
Indicates whether information on progress are printed. |
Reads tiling array data in terms of an Affymetrix BPMAP (binary probe
mapping) file and the human-readable signal.txt files that are 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 data.frame comprising all
required data on probes that are necessary for the subsequent shuffling
analysis.
Returns a data.frame containing information on all probes,
i.e., the full name of the reference sequence (organism abbreviation
and chromosome name), the chromosome name, the probe center position,
the length of the probe sequence, the GC content of the probe
sequence, the match score (if matchscore is enabled), and
the probe score.
This method is deprecated since it was specifically designed
for the Affymetrix Human tiling array 1.0R platform and the files
created by TAS. Please consider using TileReadCel or
TileReadCustom instead.