MicroarrayPreprocessConfig: Sets up a class for storing the options for preprocessing...
In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!
View source: R/preprocess_classes.R
Description
Sets up a class for storing the options for preprocessing ExpressionSets
(that is, filtering the samples and probes; adding entrez and symbol
columns)
Usage
1
2
MicroarrayPreprocessConfig(acc, entrezgene_db, keep_sample_fn = NULL,
keep_probe_fn = NULL, annot_gpl = as.logical(NA))
Arguments
acc
An identifier for the microarray dataset.
Typically this would be the GEO or ArrayExpress identifier.
entrezgene_db
A string or an OrgDB defining an
entrezgene database.
keep_sample_fn, keep_probe_fn
Functions that return a vector
of integer indices that can be used to subset an ExpressionSet. By
default, all samples and features will be kept. Can be specified as a
function literal or a "function_name" or a "pkg_name::function_name"
string. If NULL, the default functions will keep all samples or keep all
probes.
annot_gpl
Logical. Have the features in the dataset been
annotated with a GPL?
russHyde/miiq documentation built on Dec. 25, 2019, 10:56 a.m.
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View source: R/preprocess_classes.R
Description
Sets up a class for storing the options for preprocessing ExpressionSets (that is, filtering the samples and probes; adding entrez and symbol columns)
Usage
1 2 | MicroarrayPreprocessConfig(acc, entrezgene_db, keep_sample_fn = NULL,
keep_probe_fn = NULL, annot_gpl = as.logical(NA))
|
Arguments
acc |
An identifier for the microarray dataset. Typically this would be the GEO or ArrayExpress identifier. |
entrezgene_db |
A string or an |
keep_sample_fn, keep_probe_fn |
Functions that return a vector of integer indices that can be used to subset an ExpressionSet. By default, all samples and features will be kept. Can be specified as a function literal or a "function_name" or a "pkg_name::function_name" string. If NULL, the default functions will keep all samples or keep all probes. |
annot_gpl |
Logical. Have the features in the dataset been annotated with a GPL? |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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