View source: R/get_region_target_gene.R
get_region_target_gene | R Documentation |
To map an input region to genes there are three options: 1) map region to closest gene tss 2) map region to all genes within a window around the region (default window.size = 500kbp (i.e. +/- 250kbp from start or end of the region)). 3) map region to a fixed number of nearby genes (upstream/downstream)
get_region_target_gene(
regions.gr,
genome = c("hg38", "hg19"),
method = c("genes.promoter.overlap", "window", "nearby.genes", "closest.gene.tss"),
promoter.upstream.dist.tss = 2000,
promoter.downstream.dist.tss = 2000,
window.size = 500 * 10^3,
num.flanking.genes = 5,
rm.promoter.regions.from.distal.linking = TRUE
)
regions.gr |
A Genomic Ranges object (GRanges) or a SummarizedExperiment object (rowRanges will be used) |
genome |
Human genome of reference "hg38" or "hg19" |
method |
How genes are mapped to regions: region overlapping gene promoter ("genes.promoter.overlap"); or genes within a window around the region ("window"); or a fixed number genes upstream and downstream of the region ("nearby.genes"); or closest gene tss to the region ("closest.gene.tss") |
promoter.upstream.dist.tss |
Number of base pairs (bp) upstream of TSS to consider as promoter regions. Defaults to 2000 bp. |
promoter.downstream.dist.tss |
Number of base pairs (bp) downstream of TSS to consider as promoter regions. Defaults to 2000 bp. |
window.size |
When |
num.flanking.genes |
When |
rm.promoter.regions.from.distal.linking |
When performing distal linking with method = "windows", "nearby.genes" or "closest.gene.tss", if set to TRUE (default), probes in promoter regions will be removed from the input. |
For the analysis of probes in promoter regions (promoter analysis),
we recommend setting
method = "genes.promoter.overlap"
.
For the analysis of probes in distal regions (distal analysis),
we recommend setting either method = "window"
or method = "nearby.genes"
.
Note that because method = "window"
or
method = "nearby.genes"
are
mainly used for analyzing distal probes,
by default rm.promoter.regions.from.distal.linking = TRUE
to
remove probes in promoter regions.
A data frame with the following information: regionID, Target symbol, Target ensembl ID
library(GenomicRanges)
library(dplyr)
# Create example region
regions.gr <- data.frame(
chrom = c("chr22", "chr22", "chr22", "chr22", "chr22"),
start = c("39377790", "50987294", "19746156", "42470063", "43817258"),
end = c("39377930", "50987527", "19746368", "42470223", "43817384"),
stringsAsFactors = FALSE) %>%
makeGRangesFromDataFrame
# map to closest gene tss
region.genes.promoter.overlaps <- get_region_target_gene(
regions.gr = regions.gr,
genome = "hg19",
method = "genes.promoter.overlap"
)
# map to all gene within region +- 250kbp
region.window.genes <- get_region_target_gene(
regions.gr = regions.gr,
genome = "hg19",
method = "window",
window.size = 500 * 10^3
)
# map regions to n upstream and n downstream genes
region.nearby.genes <- get_region_target_gene(
regions.gr = regions.gr,
genome = "hg19",
method = "nearby.genes",
num.flanking.genes = 5
)
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