Description Usage Arguments Details Value See Also
Enables easy uploading of probeset structure & AS events to a genome browser
1 2 3 |
cdf |
an |
units |
the units to be exported |
scoreCel |
optional. An AffymetrixCelFile containing the group-level, (exon-level) scores for the given units. |
thresh |
The value above which the scores are indicated using |
singleBed |
logical. If |
upCol |
The colour to display for probesets with a positive score |
downCol |
The colour to display for probesets with a negative score |
ucscTracks |
The additional tracks to display in the UCSC browser |
... |
not used |
This function enables easy display of the unit & group (probeset) structure of a given gene, or set of genes. In the case of custom generated CDF files this can be very useful for displaying the structure.
If scores are not provided the displayed tracks will default to black,
however if scores are provided, any probesets with score above the threshold will be displayed in
colours of varying intensity, using those supplied in upCol
& downCol
.
All files with the genomic co-ordinates must also be present in the same directory as the supplied cdf. The name of this file must end with "mapping.txt" and must also contain the full cdf name somewhere in it's name.
Returns TRUE
invisibly
Files will be written to the current working directory in the .BED format.
If singleBed=TRUE
a single file will be written including the current cdf name & any tags supplied via the scoreCel file.
If singleBed=FALSE
an individual .BED file will be written for each unit.
The name will consist of any tags on the scoreCel file plus the unit ID as annotated on the cdf.
AffymetrixCelFile
, AffymetrixCdfFile
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