tabixToGr: Scan a single Tabix'ed file's ranges (only!) into a GRanges...

In trichelab/h5testR: Tests for HDF5-backed DNAme, RNAseq, and MultiAssayExperiment objects

Description

Modified from a prototype originally by Wanding Zhou (github.com/zwdzwd). One useful ... argument is yieldSize, e.g. yieldSize=1e4, to avoid wedging. Another useful ... argument is index, if not the usual tf.tbi scheme.

Usage

tabixToGr(tf, verbose = TRUE, is0based = TRUE, ...)

Arguments

tf	a tabix'ed file (either a character(1) or a TabixFile)
verbose	Provide feedback on which file is being read? (TRUE)
is0based	Are the intervals in the tabixed file 0-based? (TRUE)
...	other arguments to pass to Rsamtools::TabixFile()

Details

Beware: the parameter 'is0based' may be extremely important for your usage. It is a good idea to look at the returned GRanges object to ensure this.

Value

a GRanges

trichelab/h5testR documentation built on July 12, 2020, 5:18 p.m.