Description Usage Arguments Value
This function loads the Allen Brain Atlas reference data matrix. Different pre-defined gene lists or sample lists allow prefiltering of the loaded data.
1 2 3 4 5 | retrieveABARef(sampleSet = c("full", "fetal", "fetal_before10pcw",
"fetal_after10pcw"), geneSet = c("full", "highvar", "fetal_highvar",
"region_fetalB10", "region_fetalA10", "region_fetalB10-2",
"regionGroup_fetalB10", "regionGroup_fetalA10"), geneList = NULL,
excludeG2M = TRUE, logTransform = TRUE)
|
sampleSet |
The pre-defined sample list for output. |
geneSet |
The pre-defined gene list for output. |
geneList |
The customized gene list for output. When it is NULL, the pre-defined gene list will be used. |
excludeG2M |
When it is TRUE, G2 and M phrase marker genes will be excluded from the gene list. |
logTransform |
When it is TRUE, log-transformation with pseudo-count will be applied to the expression matrix (in RPKM). |
A list of the loaded data, in which there are three components: 'expr' is the data matrix, 'rowMeta' is the row (gene) information, and 'colMeta' is the column (reference sample) information.
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