median_summary: Compute median summaries of log ratios at a CNV region
In scristia/CNPBayes: Bayesian mixture models for copy number polymorphisms

Description Usage Arguments Details Examples

Compute median summaries of log ratios at a CNV region and define an indicator for likely deletions based on a user specified threshold for the median log ratio. The identification of likely deletions can be helpful to flag possibly rare deletions.

1	median_summary(se, provisional_batch, assay_index = 1, THR)

`se`	a SummarizedExperiment with assays containing SNP or bin-level summaries of copy number, typically log ratios.
`provisional_batch`	A provisional definition of batch. Examples include PCR data, study center, DNA source, etc. See details.
`assay_index`	If multiple assays are included in the SummarizedExperiment, the user should indicate which assay should be median summarized by a numeric index.
`THR`	numeric value indicate that log ratios below this value are potentially samples with hemizygous or homozygous deletions.

See vignette for additional details.

extdir <- system.file("extdata", package="CNPBayes")
se <- readRDS(file.path(extdir, "snp_se.rds"))
cnv_region <- GRanges("chr2", IRanges(90010895, 90248037),
                      seqinfo=seqinfo(se))
se2 <- subsetByOverlaps(se, cnv_region)
provisional_batch <- se2$Sample.Plate
full.data <- median_summary(se2,
                            provisional_batch=provisional_batch,
                            assay_index=2,
                            THR=-1)