Package 'geneClusterPattern'

Plot conserved gene pattern cross multiple species

Description

Understanding the conservation of gene neighborhoods across species provides important insights into genome organization, functional linkage, and evolutionary processes. This package is developed to facilitate the systematic characterization of orthologous gene arrangements surrounding a focal gene across multiple species. Based on the orthology information, geneClusterPattern constructs an ordered representation of genes within a configurable genomic window upstream and downstream of the focal gene. The resulting ortholog gene pattern captures the relative arrangement of ortholog groups across species, enabling direct comparison of local genomic structure.

Author(s)

Maintainer: Jianhong Ou [email protected] (ORCID)

Authors:

• Jianhong Ou [email protected] (ORCID)

• Kenneth Poss [email protected] [funder]

See Also

Useful links:

• https://github.com/jianhong/geneClusterPattern

• Report bugs at https://github.com/jianhong/geneClusterPattern/issues

---

Read Orthologues results as a list This function is under-development.

Description

Read Orthologues results as a list This function is under-development.

Usage

fromOrthogroups(orthogroups, annoGR_list, query_species = 1, split = ", ")

Arguments

orthogroups	A dataframe with the gene ids for each orthologues group
annoGR_list	A GRangesList object with the gene information. The names of each element should be contain all the gene ids saved in the orthogroups parameter. For each element, the 'gene_name' should be available in the metadata.
query_species	The species used as queryGR in getGeneCluster.
split	character vector used to split the gene ids in the dataframe of orthogroups parameter.

Value

a list of queryGR and homologsList used by getGeneCluster.

Examples

orthogroups <- read.delim(
     system.file('extdata/orthofinder/Orthogroups.tsv.gz',
                  package='geneClusterPattern'),
     row.names=1)
annoGR_list <- readRDS(
     system.file('extdata/orthofinder/grange.obj.rds',
                  package='geneClusterPattern'))
colnames(orthogroups) <- names(annoGR_list)
hres <- fromOrthogroups(orthogroups, annoGR_list)

---

Calculate the gene order score

Description

Calculate the gene order score.

Usage

geneOrderScore(
  genesList,
  ids,
  ref,
  k = length(ids),
  max_gap = 1e+07,
  method = c("edit distance", "global alignment score", "spearman correlation",
    "kendall correlation", "non-random score", "pairs distance", "pairs direction"),
  output = c("score", "value matrix")
)

Arguments

genesList	A list of GRanges.
ids	IDs to be plotted. See getGeneCluster.
ref	The reference species.
k	The maximum number of nearest genes used in getGeneCluster.
max_gap	The maximal gaps from the first ID in 'ids'.
method	The method to calculate the gene order score. 'edit distance', the gene order score is the mean of edit (Levenshtein) distance of given ids from different species. Gene order score = k/length(ids)/(mean(adist)+1). 'global alignment score', the gene order score is the mean of normalized global alignment score. For global alignment score please refer pairwiseAlignment. The alignment score will be normalized by the reference self alignment score. 'spearman correlation', the score is the mean of absolute value of Spearman correlation of the genes appearance order. 'non-random score', the score is the mean of Jaccard index of 2-order and 3-order of ids for paired samples. 'pairs distance', the score is the mean of pairwise coordinates distance. Score = k/length(ids)/(mean(abs(coordinates distance))+1). 'pairs direction', the score is the mean of alignment of pairwise strand information. The higher the gene order score, the higher the conservation of gene order.
output	Output values

Value

the score or values matrix such as adist, or alignment scores.

Examples

fish <- readRDS(system.file('extdata', 'fish.rds',
package = 'geneClusterPattern'))
homologs <- readRDS(system.file('extdata', 'homologs.rds',
                                package = 'geneClusterPattern'))
queryGene <- 'inhbaa'
nearest10neighbors <- getGeneCluster(fish, queryGene, homologs, k=10)
genesList <- c(drerio=fish, homologs)[
c("hsapiens", "mmusculus", "drerio", "olatipes", "nfurzeri", "gaculeatus")]
# set zebrafish as reference
geneOrderScore(genesList, nearest10neighbors, ref='drerio')
# default first element is reference
geneOrderScore(genesList, nearest10neighbors, method='edit distance')
geneOrderScore(genesList, nearest10neighbors, method='global alignment score')
geneOrderScore(genesList, nearest10neighbors, method='spearman correlation')
geneOrderScore(genesList, nearest10neighbors, method='kendall correlation')
geneOrderScore(genesList, nearest10neighbors, method='non-random score')
geneOrderScore(genesList, nearest10neighbors, method='pairs distance')
geneOrderScore(genesList, nearest10neighbors, method='pairs direction')

---

calculate the gene cluster

Description

A gene cluster is defined as the k nearest genes surrounding a reference gene according to the rank matrix. The rank matrix is a gene-by-species matrix, where each column contains the genomic ranks of genes for a given species.

Usage

getGeneCluster(queryGR, queryGeneName, homologsList, k = 10, radius = 0)

Arguments

queryGR	The query GRanges outputted by grangesFromEnsemblIDs.
queryGeneName	The center gene used to search.
homologsList	The homologs list outputted by getHomologGeneList.
k	The maximum number of nearest genes.
radius	The maximum number of gap genes for the search. If radius is set to greater than 0, k parameter will be ignored.

Value

The ids of the cluster for the center gene.

Examples

fish <- readRDS(system.file('extdata', 'fish.rds',
                            package = 'geneClusterPattern'))
homologs <- readRDS(system.file('extdata', 'homologs.rds',
                                package = 'geneClusterPattern'))
queryGene <- 'inhbaa'
nearestNeighbors <- getGeneCluster(fish, queryGene, homologs)

---

Get the gene position orders

Description

Get the gene position orders without considering the strand info.

Usage

getGeneRank(genes)

Arguments

genes

A GRanges object with names.

Value

A list with gene ranks named by the chromosome names.

Examples

fish <- readRDS(system.file('extdata', 'fish.rds', 
                package = 'geneClusterPattern'))
ggr <- getGeneRank(fish)

---

Get the gene positions for homologs

Description

Get the gene positions without considering the strand info.

Usage

getHomologGeneList(species, mart, ensembl_gene_ids, ...)

Arguments

species	The target species for homologs query.
mart	object of class Mart.
ensembl_gene_ids	Ensembl gene ids.
...	Parameters could be used by useEnsembl except 'biomart'.

Value

A list of GRanges objects with gene positions.

Examples

if(interactive()){
  ## Ensembl server may not response
  library(biomaRt)
  fish <- readRDS(system.file('extdata', 'fish.rds',
                            package = 'geneClusterPattern'))
  ensembl_gene_ids <- names(fish[seqnames(fish)=='24'])
  species <- c('hsapiens', 'mmusculus')
  fish_mart <- useMart("ENSEMBL_MART_ENSEMBL", "drerio_gene_ensembl")
  homologs <- getHomologGeneList(species, fish_mart, ensembl_gene_ids)
}

---

Get the gene position orders for output of OrthoFinder

Description

Get the gene position orders without considering the strand info.

Usage

getHomologListForOrthoFinder(orthologs, marts)

Arguments

orthologs	The output of orthologPairsFromOrthoFinder.
marts	a list of object of class Mart.

Value

A list of list with gene ranks named by the chromosome names.

Examples

path <- system.file('extdata/orthofinder/Danio_rerio.GRCz11.pep.all.tsv.gz',
                  package='geneClusterPattern')
orthologs <- orthologPairsFromOrthoFinder(path)
annoGR_list <- readRDS(
     system.file('extdata/orthofinder/grange.obj.rds',
                  package='geneClusterPattern'))
homologs <- getHomologListForOrthoFinder(orthologs, annoGR_list[-1])

---

create a GRanges object by given ensembl gene ids

Description

Create a GRanges object by given ensembl gene ids

Usage

grangesFromEnsemblIDs(mart, ensembl_gene_ids)

Arguments

mart	object of class Mart.
ensembl_gene_ids	Ensembl gene ids.

Value

An object of GRanges

Examples

if(interactive()){
  library(biomaRt)
  mart <- useMart('ensembl', 'drerio_gene_ensembl')
  grangesFromEnsemblIDs(mart, c('ENSDARG00000008803', 'ENSDARG00000017038'))
}

---

Guess the species

Description

Guess the species for a given string.

Usage

guessSpecies(
  species,
  output = c("abbr", "scientific name", "mart", "taxid", "common name"),
  ...
)

Arguments

species	A character(1L) to guess.
output	Output type.
...	Parameter will be passed to useEnsembl.

Value

A character or Mart object.

Examples

if(interactive()){
  guessSpecies('zebrafish')
  guessSpecies('Japanese medaka')
  guessSpecies('stickleback')
  guessSpecies('hsapiens', output='scientific name')
  guessSpecies('human', output='taxid')
  guessSpecies('hg38', output='scientific name')
  guessSpecies('hg38', output='taxid')
  guessSpecies('GRCh38', output='scientific name')
  guessSpecies('GRCh38', output='taxid')
}

---

retrieve a homologs by given ensembl gene ids

Description

This function retrieves the user specified homologs for given ensembl gene ids.

Usage

homologsFromEnsemblIDs(species, mart, ensembl_gene_ids, ...)

Arguments

species	The target species for homologs query.
mart	object of class Mart.
ensembl_gene_ids	Ensembl gene ids.
...	Parameters could be used by useEnsembl except 'biomart'.

Value

An object of GRanges

Examples

if(interactive()){
  library(biomaRt)
  mart <- useMart('ensembl', 'drerio_gene_ensembl')
  homologsFromEnsemblIDs(
    'human',
    mart,
   c('ENSDARG00000008803', 'ENSDARG00000017038'))
}

---

Read orthoFinder Orthologues results as a list Read orthoFinder Orthologues results as a list for each pair of orthologs.

Description

Read orthoFinder Orthologues results as a list Read orthoFinder Orthologues results as a list for each pair of orthologs.

Usage

orthologPairsFromOrthoFinder(path)

Arguments

path	The path of the orthologues result file.

Value

a list of matrix with the paired orthologues.

Examples

path <- system.file('extdata/orthofinder/Danio_rerio.GRCz11.pep.all.tsv.gz',
                  package='geneClusterPattern')
orthologs <- orthologPairsFromOrthoFinder(path)

---

plot gene patters for given ids

Description

Plot the gene patters for given ids.

Usage

plotGeneClusterPatterns(
  genesList,
  ids,
  additionalID,
  max_gap = 1e+07,
  colors,
  maxNonEssential = 5,
  alignType = c("local", "global"),
  label_size = 0.5
)

Arguments

genesList	A list of GRanges.
ids	IDs to be plotted. See getGeneCluster.
additionalID	Other IDs should be included.
max_gap	The maximal gaps from the first ID in 'ids'.
colors	The colors for genes
maxNonEssential	The maximal number for non-essential genes between two essential genes.
alignType	Align the gene pattern by query gene ('local') or by the clusters ('global').
label_size	The label cex value. default is 0.5.

Value

invisible list of plot data.

Examples

fish <- readRDS(system.file('extdata', 'fish.rds',
                            package = 'geneClusterPattern'))
homologs <- readRDS(system.file('extdata', 'homologs.rds',
                                package = 'geneClusterPattern'))
queryGene <- 'inhbaa'
nearestNeighbors <- getGeneCluster(fish, queryGene, homologs)
genesList <- c(drerio=fish, homologs)
pgp <- plotGeneClusterPatterns(genesList, nearestNeighbors)

---

Drop non-standard chromosomes Remove the unwanted chromosomes from a list of GRanges object.

Description

Drop non-standard chromosomes Remove the unwanted chromosomes from a list of GRanges object.

Usage

pruningSequences(genesList, negativePattern = "[_.M]")

Arguments

genesList	A list of GRanges object
negativePattern	The pattern to match the seqnames that does not need.

Value

A list of filtered GRanges

Examples

library(GenomicRanges)
gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))
pruningSequences(list(gr))

---