subsetByOverlaps-rseHandle-GRanges-method: Subset an 'rseHandle' object by region defined in a 'GRanges'...

In caleblareau/yolo: You Only Lookup One (small part of an otherwise large matrix)

Description

Subset an rseHandle object by region defined in a GRanges object

Usage

## S4 method for signature 'rseHandle,GRanges'
subsetByOverlaps(query, subject, maxgap = 0L,
  minoverlap = 1L, type = c("any", "start", "end", "within", "equal"),
  invert = FALSE, ...)

Arguments

query	An rseHandle object
subject	A GRanges object of the regions of intrest
maxgap	Refer to GRanges documentation of this function.
minoverlap	Refer to GRanges documentation of this function.
type	Refer to GRanges documentation of this function.
invert	Refer to GRanges documentation of this function.
...	Refer to GRanges documentation of this function.

Value

A rseHandle object subsetted after the subjet was filtered

Examples

library(GenomicRanges)
chr12reg <- GRanges(seqnames=c("chr12"),
     ranges = IRanges(start=c(56150000),end=c(56500000)))
dat2 <- readRDS(system.file("rds", "dat2_ssh.rds", package = "yolo"))
ss <- subsetByOverlaps(dat2, chr12reg)

caleblareau/yolo documentation built on May 13, 2019, 11:01 a.m.