MapRangesToGenomicIntervals: MapRangesToGenomicIntervals

In favorov/GenometriCorr: Genometric Correlation package

Description

MapRangesToGenomicIntervals collapses all the chromosomes to their subsets covered by where.to.map and then liftover the what.to.map to this genome subset. The function is intended to prepare an estimation correlation of two features that are spatially restricted in the genome. We map them both to their location areas (the where.to.map is common for query and for the rerefence), and then we calculate the GenometriCorrelation between the mapped fatures.)

Usage

MapRangesToGenomicIntervals(
  where.to.map,
  what.to.map,
  chrom.suffix = "_mapped",
  chromosomes.to.proceed = NA,
  chromosomes.length = c(),
  unmapped.chromosome.warning = TRUE,
  nonnormalised.mapping.warning = TRUE
)

Arguments

where.to.map	The set of genomic intervals we map to.
what.to.map	The set of ranges that we map.
chrom.suffix	The suffix to be appended to all the sestination chromosome names in the mapping; default is "_mapped".
chromosomes.to.proceed	The default set of chromosomes to map is the intersection of the chromosomes in where.to.map and what.to.map. If we want to restrict the set, we can do it with this parameter.
chromosomes.length	is an alternative to seqingo() ot the GRanges of where.to.map way to pass the lengths of chromosomes to the mapping routine
unmapped.chromosome.warning	For each chromosome that is represented in what.to.map and that is included in chromosomes.to.proceed if it is given and that is not represented in where.to.map, a warning is generated if unmapped.chromosome.warning is TRUE. The default is TRUE.
nonnormalised.mapping.warning	If the input mapping space is not normalised (e.g. contains overlapping intervals), it is normalised before the mapping. A warning is generated if nonnormalised.mapping.warning is TRUE. The default is TRUE.

Value

GRanges object that is a liftover of what.to.map to subgenome covered by where.to.map

Author(s)

Alexander Favorov [e-mail], Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Veronica Busa, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan.

References

GenometriCorr home

See Also

The GenometriCorr documentation and vignette.

Examples

library('GenometriCorr')
intervals<-GRanges(ranges=IRanges(c(1,10001,1,10001),width=c(1000)),seqnames=c('chr1','chr1','chr2','chr2'),seqlengths=c('chr1'=300000,'chr2'=300000))
ranges=GRanges(ranges=IRanges(c(10,110,10101,100000,500,550,1055),width=c(10)),seqnames=c(rep('chr1',4),rep('chr2',3)),seqlengths=c('chr1'=300000,'chr2'=300000))
mapped<-MapRangesToGenomicIntervals(where.to.map=intervals,what.to.map=ranges)

favorov/GenometriCorr documentation built on March 30, 2021, 5:21 p.m.