getGeneNeighborhood: Extract info on upstream and downstream features/genes

In pgpmartin/GeneNeighborhood: Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Description

Get orientation and distance info on the upstream and downstream features/genes from a GRanges

Usage

getGeneNeighborhood(GeneGRanges)

Arguments

GeneGRanges

A GRanges of feature/gene annotations

Value

A tibble with the following columns:

• GeneName: Name of the focus gene

• Chr: Seqnames of the focus gene

• Strand: Strand of the focus gene

• Precede: Name of the gene that the focus gene precedes (ignoring strand info)

• Follow: Name of the gene that the focus gene follows (ignoring strand info)

• Upstream: Name of the gene located upstream of the focus gene

• Downstream: Name of the gene located downstream of the focus gene

• StrandUpstream: Strand of the gene located upstream of the focus gene

• StrandDownstream: Strand of the gene located downstream of the focus gene

• UpstreamOrientation: Orientation of the upstream gene relative to the focus gene (S=same strand, O=Opposite strand or other)

• DownstreamOrientation: Orientation of the downstream gene relative to the focus gene (S, O or other)

• UpstreamDistance: Distance between the focus gene and its upstream neighbor

• DownstreamDistance: Distance between the focus gene and its downstream neighbor

• CountOvlAnyStrand: Number of genes with which the focus gene overlaps

• ovlType: Type of overlaps (see DETAILS)

• ovlGene: Name of the gene with which the focus gene overlaps (when it overlaps with a single gene)

• NeighborClass: Class of gene neighborhood (see DETAILS)

• UpstreamClass: Class of upstream Neighborhood (takes into account the presence of an overlap)

• DownstreamClass: Class of downstream Neighborhood (takes into account the presence of an overlap)

• GenePair: Type of gene pair formed between the focus gene and the gene that follows (see DETAILS)

• Distance2Pair: Intergenic distance between the focus gene and the gene that follows

DETAILS

Up/DownstreamOrientation columns do not precise if the up/downstream gene overlaps with the focus gene.

A distance of 0 in Up/DownstreamDistance columns can indicate that the genes overlap or that they are adjacent.

The type of overlaps in the ovlType column are coded as follow:

• c. The focus gene overlaps with more than 1 gene ("complex" overlap pattern)

• I. The focus gene shares the same borders (start AND end) with a gene on the same strand

• i. The focus gene shares the same borders (start AND end) with a gene on the opposite strand

• H. The focus gene "hosts" (=contains entirely) a gene on the same strand

• h. The focus gene "hosts" (=contains entirely) a gene on the opposite strand

• G. The focus gene is the "guest" of (=is entirely contained within) a gene that is on the same strand

• g. The focus gene is the "guest" of (=is entirely contained within) a gene that is on the opposite strand

• U. The 5' end of the focus gene (TSS) overlaps with a gene that is on the same strand

• u. The 5' end of the focus gene (TSS) overlaps with a gene that is on the opposite strand

• D. The 3' end of the focus gene (TES) overlaps with a gene that is on the same strand

• d. The 3' end of the focus gene (TES) overlaps with a gene that is on the opposite strand

The Neighborclass column is defined as follow:

• In the absence of overlap: A 2-letter code using S (Same Strand) and O (Opposite Strand) to indicate the orientation of the uptstream (first letter) and downstream genes (second letter)

• When ovlType is u/U or d/D: ovlType is combined with the information on the downstream (resp. upstream) gene to form the code (e.g. uS or uO)

• In all other cases: NeighborClass is equal to ovlType

The codes in the GenePair column are defined as follow:

• H2H: Head-to-Head orientation: <— —>

• T2H: Tail-to-Head orientation: —> —>

• T2T: Tail-to-Tail orientation: —> <—

Author(s)

Pascal GP Martin

Examples

## Not run: 
library(TxDb.Athaliana.BioMart.plantsmart25)
GeneNeighbors <- getGeneNeighborhood(GenomicFeatures::genes(TxDb.Athaliana.BioMart.plantsmart25))
# There are 155 genes (0.461%) that overlap with >1 gene
table(GeneNeighbors$NeighborClass)
#
#   c    g    G    h    H    i    I   Od   OD   OO   OS   Sd   SD   SO   SS   uO   UO   uS   US
# 155  257  137  190   92    4   64 1448   52 6203 7461 1415   65 6237 9358  152   37  196   65
table(table(GeneNeighbors$GenePair))
#
#  H2H   T2H   T2T
# 7762 17173  7754

## End(Not run)


set.seed(123)
#The package includes a \code{GRanges} named Genegr with 676 random genes on a single chromosome:
  Genegr

#Extract info on the neighbors of these genes:
  GeneNeighbors <- getGeneNeighborhood(Genegr)

#Classes of neighborhoods:
  table(GeneNeighbors$NeighborClass)
#Classes of gene pairs:
  table(GeneNeighbors$GenePair)

#Up/DownstreamOrientation columns don't document overlaps of the upstream/downstream gene:
  table(GeneNeighbors$NeighborClass[GeneNeighbors$UpstreamOrientation=="O"])
#This information is present in the Up/DownstreamClass columns:
  table(GeneNeighbors$NeighborClass[GeneNeighbors$DownstreamClass=="OppositeOverlap"])

pgpmartin/GeneNeighborhood documentation built on Sept. 2, 2021, 6:37 a.m.