getRegionNearGenes: Identifies nearest genes to a region
In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation
View source: R/GetNearbyGenes.R
getRegionNearGenes R Documentation
Identifies nearest genes to a region
Description
Auxiliary function for GetNearGenes
This will get the closest genes (n=numFlankingGenes) for a target region (TRange)
based on a genome of refenrece gene annotation (geneAnnot). If the
transcript level annotation (tssAnnot) is provided the Distance will be updated to
the distance to the nearest TSS.
Usage
getRegionNearGenes(
TRange = NULL,
numFlankingGenes = 20,
geneAnnot = NULL,
tssAnnot = NULL
)
Arguments
TRange
A GRange object contains coordinate of targets.
numFlankingGenes
A number determine how many gene will be collected from each
geneAnnot
A GRange object contains gene coordinates of for human genome.
tssAnnot
A GRange object contains tss coordinates of for human genome.
Value
A data frame of nearby genes and information: genes' IDs, genes' symbols,
Author(s)
Tiago C Silva (maintainer: tiagochst@usp.br)
gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.
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View source: R/GetNearbyGenes.R
| getRegionNearGenes | R Documentation |
Identifies nearest genes to a region
Description
Auxiliary function for GetNearGenes This will get the closest genes (n=numFlankingGenes) for a target region (TRange) based on a genome of refenrece gene annotation (geneAnnot). If the transcript level annotation (tssAnnot) is provided the Distance will be updated to the distance to the nearest TSS.
Usage
getRegionNearGenes(
TRange = NULL,
numFlankingGenes = 20,
geneAnnot = NULL,
tssAnnot = NULL
)
Arguments
TRange |
A GRange object contains coordinate of targets. |
numFlankingGenes |
A number determine how many gene will be collected from each |
geneAnnot |
A GRange object contains gene coordinates of for human genome. |
tssAnnot |
A GRange object contains tss coordinates of for human genome. |
Value
A data frame of nearby genes and information: genes' IDs, genes' symbols,
Author(s)
Tiago C Silva (maintainer: tiagochst@usp.br)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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