aracne | R Documentation |
This function takes in a gene expression matrix of gene expression and applies the ARACNE gene co-expression network analysis frame work to find coexpressed gene pairs in the matrix. The ARACNE framework is also installed from within the package located in the 'inst/tools/' direcctory. For more information on the ARACNE framework see: <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-S1-S7>
aracne( data, path = NULL, pval = NULL, outputpath, na_fill = NULL, tool_storage_loc )
data |
Required. The gene expression matrix with rows as sample IDs and columns as Gene or feature IDs |
path |
Optional. String containing the path to the aracne compiled executable. (Default = NULL) |
pval |
Optional. Cutoff p-value to determine a coexpressed edge. (Default = 0.05) |
outputpath |
Required. The path the resulting network should be saved to. |
na_fill |
Optional. Value to replace 'NA' values with ideally, a large negative number or use min(data). (Default = NULL) |
tool_storage_loc |
Required. Provides the directory inside docker to temporarily store the ARACNE files and package. (Default = config$input_profile$temp_storage_loc) |
A Co-Expression Network saved to the path 'outputpath' and titled 'aracneThresholdNetwork.csv' (if 'pval' < 1) or as 'aracneNetwork.csv' if 'pval' is set to 1.
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