collapseAt: Collapse a SummarizedExperiment-like object over a GRanges

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

Collapse a SummarizedExperiment-like object over a GRanges

Description

Collapse a SummarizedExperiment-like object over a GRanges

Usage

collapseAt(
  x,
  y,
  how = c("medians", "means"),
  minprobes = 2,
  imp = TRUE,
  obj = FALSE
)

Arguments

x	anything descended from a SummarizedExperiment
y	regions to summarize over, as a GRanges
how	medians or means? (medians)
minprobes	minimum probes to summarize over (1)
imp	impute any remaining NAs? (FALSE)
obj	return an object resembling x? (FALSE)

Details

No imputation is performed and only unique ranges are summarized. If you want to disjoin ranges, do it before running this function. The function just takes whatever is in assays(x)[1] and summarizes that.

Value

     an object with same colData but with new rowRanges & assays

ttriche/sesamizeGEO documentation built on Nov. 12, 2023, 5:42 p.m.