Performs a variance components estimate for each deletion allele based on the replicate metadata provided.
Performs a variance components estimate for each deletion allele based on the replicate metadata provided.
get_variance_components( del_result, replicates, allele_min_reads = 100, allele_min_fraction = 0.001 )
del_result |
The result from deletion_analysis |
replicates |
A data.frame defining GenIE replicate metadata. |
allele_min_reads |
The minimum number of reads that a deletion allele must have across all replicates to be included. |
allele_min_fraction |
The minimum fraction of total reads that a deletion allele must have across all replications to be included. |
Returns a list with tables vp_cDNA and vp_gDNA, which partition variance according to the metadata columns that begin with "replicate_" in the 'replicates' parameter.
# Note: First run deletion_analysis() # The below isn't run since it can take 10+ seconds to run # mul1_del_results is a pre-loaded result vc = get_variance_components(mul1_del_results[[1]], mul1_replicates) variance_components_plot(vc)
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