get_variance_components: Performs a variance components estimate for each deletion...

In rgenie: Analysis of GenIE Experiments

Description

Performs a variance components estimate for each deletion allele based on the replicate metadata provided.

Usage

get_variance_components(
  del_result,
  replicates,
  allele_min_reads = 100,
  allele_min_fraction = 0.001
)

Arguments

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.

Value

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.

See Also

deletion_analysis

variance_components_plot

Examples

# 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)

rgenie documentation built on Oct. 23, 2020, 8:21 p.m.