retrieveABARef: Load the Allen Brain Atlas reference set

Description Usage Arguments Value

View source: R/RSS.r

Description

This function loads the Allen Brain Atlas reference data matrix. Different pre-defined gene lists or sample lists allow prefiltering of the loaded data.

Usage

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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)

Arguments

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).

Value

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.


maplesword/RefSimSpec documentation built on Nov. 23, 2018, 12:24 a.m.