subsetByOverlaps.keepAllMeta: Help functions for handling gene ranges

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Keep all meta data when overlapping gene ranges or converting to dataframe.

Usage

subsetByOverlaps.keepAllMeta(
  gr1,
  gr2,
  write.ranges.tofile = NULL,
  addStart = 0
)

granges2df(gr1, addStart = 0)

Arguments

gr1, gr2	GRanges object
write.ranges.tofile	character with file path. If given, a data.frame is generated from the returned GRanges object and written to this destination. Omitted if NULL.
addStart	numeric with mumber of bases to be added to the start coordinate when converting a GRanges object to a dataframe. E.g. necessary for switching between 0-based and 1-based genome coordinate systems.

Details

By default, meta data is lost when GRanges are merged or overlapped. subsetByOverlaps.keepAllMeta returns overlap of two GRanges objects with merged meta data from both. Meta data stored in CompressedCharacterList is collapsed to a single column. granges2df generates a data.frame from an GRanges containing the meta data. Meta data stored in CompressedCharacterList is collapsed to a single column.

Value

subsetByOverlaps.keepAllMeta returnes GRanges object containing overlap and meta data from input ranges. granges2df returns a data.frame with genomic coordinates and meta data from input object.

Functions

• subsetByOverlaps.keepAllMeta: subsetByOverlaps which keeps meta data from both objects

• granges2df: Convert GRanges object to dataframe

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.