Description Usage Arguments Details Value Remapping indices File format Author(s) See Also Examples
Reads an Affymetrix probe data (APD) file.
1 2 3 |
filename |
The filename of the APD file. |
indices |
An optional |
readMap |
A |
name |
The name of the data field.
If |
... |
Not used. |
verbose |
See |
.checkArgs |
If |
To read one large contiguous block of elements is faster than to read individual elements one by one. For this reason, internally more elements than requested may be read and therefore allocation more memory than necessary. This means, in worst case N elements may read allocation N*8 bytes of R memory, although only two elements are queried. However, to date even with the largest arrays from Affymetrix this will still only require tens of megabytes of temporary memory. For instance, Affymetrix Mapping 100K arrays holds 2,560,000 probes requiring 20Mb of temporary memory.
A named list
with the two elements header
and
data
. The header is in turn a list
structure and
the second is a numeric
vector
holding the queried data.
Argument readMap
can be used to remap indices. For instance,
the indices of the probes can be reorder such that the probes within
a probeset is in a contiguous set of probe indices. Then, given that
the values are stored in such an order, when reading complete probesets,
data will be access much faster from file than if the values were
scatter all over the file.
Example of speed improvements. Reading all 40000 values in units 1001 to 2000 of an Affymetrix Mapping 100K Xba chip is more than 10-30 times faster with mapping compared to without.
The file format of an APD file is identical to the file format of an
FileVector
.
Henrik Bengtsson
createApd
() and updateApd
().
See also readApdHeader
().
To create a cell-index read map from an CDF file, see
readCdfUnitsWriteMap
.
1 | ## Not run: #See ?createApd for an example.
|
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