summarize_region: Wrapper for summarizing CNV regions
In scristia/CNPBayes: Bayesian mixture models for copy number polymorphisms

Description Usage Arguments Details See Also

Computes a median summary of log ratios for each sample at CNV regions, identifies batches from the provisional batch labels, and down samples the resulting summarized data for subsequent evaluation by finite mixture models.

summarize_region(
  se,
  provisional_batch,
  THR = -1,
  assay_index = 1,
  KS_cutoff = 0.001,
  S = 1000,
  min_size = 250
)

`se`	A SummarizedExperiment containing log ratios at SNPs or genomic bins for a collection of samples at a single CNV region
`provisional_batch`	A provisional batch label such as date of PCR, study center, or DNA source.
`THR`	log ratios below this value are potentially hemizygous or homozygous deletions
`assay_index`	index of the assay element in the SummarizedExperiment object that contains the log ratios that are to be summarized.
`KS_cutoff`	Cutoff for Kolmogorov-Smirnov (KS) p-value. For two batches that have a KS p-value above this threshold, the batches are combined to form a single batch.
`S`	desired number of samples to include in the down-sampled dataset
`min_size`	integer indicating the number of samples to randomly select for each batch. The actual number of samples included may be larger as samples flagged as likely deleted are not down-sampled.

Helpful to provide a provisional batch label that is fairly granular, allowing 'kolmogorov_batches' to provide a further coarsening of the batch labels.

kolmogorov_batches median_summary down_sample2 MultiBatch

scristia/CNPBayes documentation built on Aug. 9, 2020, 7:31 p.m.