#' Given genes that fall in a given upstream and downstream region of
#' mRNAs of interest, GO term enrichment analysis is carried out
#'
#' @param gene Input genes other than miRNA
#' @param org_assembly Genome assembly of interest for the analysis. Possible
#' assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat,
#' "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and
#' "hg38" for human
#' @param near Boolean value presents whether cis-neighbourhood should be
#' considered in the analysis
#' @param genetype Type of the input gene list. Possible values are "Entrez",
#' "mirna", "Ensembl_gene", "Ensembl_trans", "NCBI". For HUGO gene symbol
#' "NCBI" value, for Entrez gene id "Entrez" is used.
#' @param TAD TAD genomic regions for the species. Predefined TAD regions or
#' any new TAD regions can be used for the analysis. TAD regions must be
#' formated as GRanges object. Predefined TAD regions are 'tad_hg19',
#' 'tad_hg38', 'tad_mm10', 'tad_dmel' for hg19, hg38, mm9 and dm6
#' assembly, respectively.
#' @param isTADSearch Boolean value that shows whether TAD analysis is
#' performed. This value has to be TRUE for TAD analysis.
#' @param backG The set of genes that tested against to the input
#' (background gene)
#' @param backGType Type of the background gene. If miRNA gene set is used for
#' background gene, backGType should be set to the 'mirna'
#' @param express Boolean variable whether co-expression analysis is performed.
#' If this option is set to TRUE, co-expression analysis will be
#' performed.
#' @param isCustomExp Boolean variable whether co-expression analysis with
#' custom data will be performed. When this option is set, exp1 and exp2
#' parameters must be defined.
#' @param cancer Defines the name of the TCGA project code such as 'BRCA' for
#' correlation analysis. Possible cancer types ACC, BLCA, BRCA, CESC,
#' CHOL, COAD, COADREAD, DLBC, ESCA, GBMLGG, HNSC, KICH, KIPAN, KIRC,
#' KIRP, LGG, LIHC, LUAD, LUSC, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM,
#' STAD, STES, TGCT, THCA, THYM, UCEC, UCS, UVM
#' @param exp1 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param exp2 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param label1 Gene names of the custom exp1 expression data. If it is not
#' provided, column name of the exp1 data will be taken.
#' @param label2 Gene names of the custom exp2 expression data. If it is not
#' provided, column name of the exp2 data will be taken.
#' @param databaseFile Path of miRcancer.db file
#' @param isUnionCorGene Boolean value that shows whether union of the output
#' of the co-expression analysis and the other analysis should be
#' considered
#'
#' @return GO term enrichment object for the given input
#'
#'
#' @examples
#' ncGO<-geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly='hg19',
#' near=TRUE, genetype = 'Ensembl_gene')
#'
#' @export
geneGOEnricher <-
function(gene,
org_assembly = c("hg19",
"hg38",
"mm10",
"dre10",
"rn6",
"dm6",
"ce11",
"sc3"),
genetype = c("Entrez",
"mirna",
"Ensembl_gene",
"Ensembl_trans",
"NCBI"),
backG = '',
backGType = 'pc_gene',
near = FALSE,
isTADSearch = FALSE,
TAD = c(tad_hg19, tad_dmel, tad_hg38, tad_mm10),
express = FALSE,
isCustomExp = FALSE,
cancer,
exp1,
exp2,
label1 = '',
label2 = '',
isUnionCorGene = FALSE,
databaseFile) {
if (missing(gene))
message("Gene is missing?")
if (!is.data.frame(gene) &
!is.character(gene) & !is.factor(gene))
message("Type of the gene should be data.frame or character")
if (missing(org_assembly))
message("Assembly version is missing?")
if (missing(genetype))
message("Input gene type is missing.")
if (class(pkg.env$mart)[1] != "Mart") {
assembly(org_assembly)
}
gene <- as.data.frame(gene)
colnames(gene) <- c("genes")
geneLoc <-
convertGeneID(
genetype = genetype,
genelist = gene$genes,
org_assembly = org_assembly
)
if (near) {
ifelse(
pkg.env$searchRegion == 'all',
nearGene <-
getUCSC(
bedfile = geneLoc,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
ifelse(
pkg.env$searchRegion == 'exon',
nearGene <-
getNearToExon(
bedfile = geneLoc,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
nearGene <-
getNearToIntron(
bedfile = geneLoc,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
)
)
)
}
else{
nearGene <-
getUCSC(
bedfile = geneLoc,
upstream = 0,
downstream = 0,
org_assembly = org_assembly
)
}
if (isTADSearch) {
tadGene <-
getTADOverlap(
bedfile = geneLoc,
tad = TAD,
cellline = pkg.env$cellline,
org_assembly = org_assembly,
near = near,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream
)
if (near)
nearGene <-
as.data.frame(intersect(unlist(nearGene), unlist(tadGene)))
else
nearGene <- tadGene
}
if (express) {
if (!isCustomExp) {
nearG <-
corrbasedMrna(
mRNAgene = nearGene,
cancer = cancer,
minAbsCor = pkg.env$minAbsCor,
databaseFile = databaseFile
)
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$feature)
else
nearGene <- union(unlist(nearGene), nearG$feature)
}
else{
nearG <- calculateCorr(
exp1 = exp1,
exp2 = exp2,
label1 = label1 ,
label2 = label2,
corrMethod = pkg.env$corrMethod,
varCutoff = pkg.env$varCutoff,
corCutoff = pkg.env$minAbsCor,
pcut = pkg.env$pcut,
alternate = pkg.env$alternate,
conf = pkg.env$conf
)
tt <- lapply(seq_len(length(gene$genes)), function(x)
unlist(which(nearG$firstExp %in% (gene$genes[x]))))
nearG <- nearG[unlist(tt), ]
if (!isUnionCorGene)
nearGene <-
intersect(unlist(nearGene), unlist(nearG$SecondExp))
else
nearGene <-
union(unlist(nearGene), unlist(nearG$SecondExp))
}
}
if (length(nearGene) == 0) {
message("No common gene is found")
methods::new(
"NoRCE",
ID = '',
Term = '',
geneList = list(),
pvalue = 0,
pAdj = 0,
GeneRatio = '',
BckRatio = ''
)
}
else{
enrichedGene <-
goEnrichment(
genes = nearGene,
GOtype = pkg.env$GOtype,
org_assembly = org_assembly,
pCut = pkg.env$pCut,
pAdjCut = pkg.env$pAdjCut,
pAdjust = pkg.env$pAdjust,
backG = backG,
backGType = backGType,
enrichTest = pkg.env$enrichTest,
min = pkg.env$min
)
if (length(enrichedGene@Term) > 0)
{
enrichedGene@ncGeneList <- commonGene(
mrnaobject = enrichedGene,
org_assembly = org_assembly,
downstream = pkg.env$downstream,
upstream = pkg.env$upstream,
inputGene = gene$genes,
inGeneType = genetype
)
}
return(enrichedGene)
}
}
#' Given genes that fall in the given upstream and downstream region of
#' mRNAs of interest, pathway enrichment analysis is carried out
#'
#' @param gene Input noncoding genes other than miRNA
#' @param org_assembly Genome assembly of interest for the analysis. Possible
#' assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat,
#' "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and
#' "hg38" for human
#' @param genetype Type of the input gene list. Possible values are "Entrez",
#' "mirna", "Ensembl_gene", "Ensembl_trans", "NCBI". For HUGO gene symbol
#' "NCBI" value, for Entrez gene id "Entrez", for mirbase id "mirna" is
#' used.
#' @param near Boolean value presents whether cis-neighbourhood should be
#' considered in the analysis
#' @param isTADSearch Boolean value that shows whether TAD analysis is
#' performed. This value has to be TRUE for TAD analysis.
#' @param TAD TAD genomic regions for the species. Predefined TAD regions or
#' any new TAD regions can be used for the analysis. TAD regions must be
#' formated as GRanges object. Predefined TAD regions are 'tad_hg19',
#' 'tad_hg38', 'tad_mm10', 'tad_dmel' for hg19, hg38, mm9 and dm6
#' assembly, respectively.
#' @param gmtName Custom pathway gmt file
#' @param express Boolean variable whether co-expression analysis is performed.
#' If this option is set to TRUE, co-expression analysis will be
#' performed.
#' @param isCustomExp Boolean variable whether co-expression analysis with
#' custom data will be performed. When this option is set, exp1 and exp2
#' parameters must be defined.
#' @param cancer Defines the name of the TCGA project code such as 'BRCA' for
#' correlation analysis. Possible cancer types ACC, BLCA, BRCA, CESC,
#' CHOL,COAD, COADREAD, DLBC, ESCA, GBMLGG, HNSC, KICH, KIPAN, KIRC, KIRP,
#' LIHC, LUAD, LUSC, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM, STAD, STES,
#' TGCT, THCA, THYM, UCEC, UCS, UVM, LGG
#' @param exp1 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param exp2 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param label1 Gene names of the custom exp1 expression data. If it is not
#' provided, column name of the exp1 data will be taken.
#' @param label2 Gene names of the custom exp2 expression data. If it is not
#' provided, column name of the exp2 data will be taken.
#' @param databaseFile Path of miRcancer.db file
#' @param isUnionCorGene Boolean value that shows whether union of the output
#' of the co-expression analysis and the other analysis should be
#' considered
#' @param isGeneEnrich Boolean value whether gene enrichment should be
#' performed
#'
#' @return Pathway enrichment object for the given input
#'
#'
#' @examples
#' #Pathway enrichment based on the gen sets that falls into the TAD regions
#' ncRNAPathway<-genePathwayEnricher(gene = brain_disorder_ncRNA ,
#' org_assembly='hg19',
#' isTADSearch = TRUE,
#' TAD = tad_hg19,
#' genetype = 'Ensembl_gene')
#'
#'
#' @export
genePathwayEnricher <-
function(gene,
org_assembly = c("hg19",
"hg38",
"mm10",
"dre10",
"rn6",
"dm6",
"ce11",
"sc3"),
genetype = c("Entrez",
"mirna",
"Ensembl_gene",
"Ensembl_trans",
"NCBI"),
near = TRUE,
isTADSearch = FALSE,
TAD = tad_hg19,
gmtName = '',
express = FALSE,
isCustomExp = FALSE,
cancer,
exp1,
exp2,
label1 = '',
label2 = '',
isUnionCorGene = FALSE,
databaseFile,
isGeneEnrich = FALSE) {
if (missing(gene)) {
message("Gene is missing?")
}
if (!is.data.frame(gene) &
!is.character(gene) & !is.factor(gene))
message("Type of the gene should be data.frame or character")
if (missing(org_assembly)) {
message("Assembly version is missing?")
}
if (class(pkg.env$mart)[1] != "Mart") {
assembly(org_assembly)
}
if (missing(genetype))
message("Input gene type is missing.")
gene <- as.data.frame(gene)
colnames(gene) <- c("genes")
geneLoc <-
convertGeneID(
genetype = genetype,
genelist = gene$genes,
org_assembly = org_assembly
)
if (near) {
ifelse(
pkg.env$searchRegion == 'all',
nearGene <-
getUCSC(
bedfile = geneLoc,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
ifelse(
pkg.env$searchRegion == 'exon',
nearGene <-
getNearToExon(
bedfile = geneLoc,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
nearGene <-
getNearToIntron(
bedfile = geneLoc,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
)
)
)
}
else{
nearGene <-
getUCSC(
bedfile = geneLoc,
upstream = 0,
downstream = 0,
org_assembly = org_assembly
)
}
if (isTADSearch) {
tadGene <-
getTADOverlap(
bedfile = geneLoc,
tad = TAD,
cellline = pkg.env$cellline,
org_assembly = org_assembly,
near = near,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream
)
if (near)
nearGene <-
as.data.frame(intersect(unlist(nearGene), unlist(tadGene)))
else
nearGene <- tadGene
}
if (express) {
if (!isCustomExp) {
nearG <-
corrbasedMrna(
mRNAgene = nearGene,
cancer = cancer,
minAbsCor = pkg.env$minAbsCor,
databaseFile = databaseFile
)
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$feature)
else
nearGene <- union(unlist(nearGene), nearG$feature)
}
else{
nearG <- calculateCorr(
exp1 = exp1,
exp2 = exp2,
label1 = label1 ,
label2 = label2,
corrMethod = pkg.env$corrMethod,
varCutoff = pkg.env$varCutoff,
corCutoff = pkg.env$minAbsCor,
pcut = pkg.env$pcut,
alternate = pkg.env$alternate,
conf = pkg.env$conf
)
tt <- lapply(seq_len(nrow(gene$genes)), function(x)
unlist(which(nearG$firstExp %in% (gene$genes[x]))))
nearG <- nearG[unlist(tt), ]
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$SecondExp)
else
nearGene <- union(unlist(nearGene), nearG$SecondExp)
}
}
if (length(nearGene) == 0) {
message("No common gene is found")
methods::new(
"NoRCE",
ID = '',
Term = '',
geneList = list(),
pvalue = 0,
pAdj = 0,
GeneRatio = '',
BckRatio = ''
)
}
else{
ifelse(
pkg.env$pathwayType == 'kegg',
pth <- 1,
ifelse(
pkg.env$pathwayType == 'reactome',
pth <- 2,
ifelse(pkg.env$pathwayType == 'wiki',
pth <- 3,
pth <- 4)
)
)
ifelse(
pkg.env$pathwayType == 'kegg',
pth <- 1,
ifelse(
pkg.env$pathwayType == 'reactome',
pth <- 2,
ifelse(pkg.env$pathwayType == 'wiki',
pth <- 3,
pth <- 4)
)
)
funclist <- list(KeggEnrichment,
reactomeEnrichment,
WikiEnrichment,
pathwayEnrichment)
enrichedGene <- funclist[[pth]](
genes = nearGene,
gmtFile = gmtName,
org_assembly = org_assembly,
pCut = pkg.env$pCut,
pAdjCut = pkg.env$pAdjCut,
pAdjust = pkg.env$pAdjust,
isSymbol = pkg.env$isSymbol,
min = pkg.env$min,
isGeneEnrich = isGeneEnrich
)
if (length(enrichedGene@Term) > 0)
{
enrichedGene@ncGeneList <- commonGene(
mrnaobject = enrichedGene,
org_assembly = org_assembly,
downstream = pkg.env$downstream,
upstream = pkg.env$upstream,
inputGene = gene$genes,
inGeneType = genetype
)
}
return(enrichedGene)
}
}
#' Given gene regions that fall in the given upstream and downstream region
#' of mRNAs of interest, GO term enrichment analysis is carried out
#'
#' @param region Bed format of the input gene regions other than miRNA
#' @param org_assembly Genome assembly of interest for the analysis. Possible
#' assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat,
#' "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and
#' "hg38" for human
#' @param near Boolean value presents whether cis-neighbourhood should be
#' considered in the analysis
#' @param isTADSearch Boolean value that shows whether TAD analysis is
#' performed. This value has to be TRUE for TAD analysis.
#' @param TAD TAD genomic regions for the species. Predefined TAD regions or
#' any new TAD regions can be used for the analysis. TAD regions must be
#' formated as GRanges object. Predefined TAD regions are 'tad_hg19',
#' 'tad_hg38', 'tad_mm10', 'tad_dmel' for hg19, hg38, mm9 and dm6
#' assembly, respectively.
#' @param backG The set of genes that tested against to the input
#' (background gene)
#' @param backGType Type of the background gene. If miRNA gene set is used for
#' background gene, backGType should be set to the 'mirna'
#' @param express Boolean variable whether co-expression analysis is
#' performed. If this option is set to TRUE, co-expression analysis will
#' be performed.
#' @param isCustomExp Boolean variable whether co-expression analysis with
#' custom data will be performed. When this option is set, exp1 and exp2
#' parameters must be defined.
#' @param cancer Defines the name of the TCGA project code such as 'BRCA' for
#' correlation analysis. Possible cancer types ACC, BLCA, BRCA, CESC,
#' CHOL, COAD, COADREAD, DLBC, ESCA, GBMLGG, HNSC, KICH, KIPAN, KIRC,
#' KIRP, LGG, LIHC, LUAD, LUSC, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM,
#' STAD, STES, TGCT, THCA, THYM, UCEC, UCS, UVM
#' @param exp1 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param exp2 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param label1 Gene names of the custom exp1 expression data. If it is not
#' provided, column name of the exp1 data will be taken.
#' @param label2 Gene names of the custom exp2 expression data. If it is not
#' provided, column name of the exp2 data will be taken.
#' @param databaseFile Path of miRcancer.db file
#' @param isUnionCorGene Boolean value that shows whether union of the output
#' of the co-expression analysis and the other analysis should be
#' considered
#'
#'
#' @return GO term enrichment object for the given input
#'
#' @importFrom rtracklayer import
#' @examples
#'
#' regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")
#' regionNC <- rtracklayer::import(regions, format = "BED")
#' regionGO<-geneRegionGOEnricher(region = regionNC, org_assembly= 'hg19',
#' near = TRUE)
#'
#' @export
geneRegionGOEnricher <-
function(region,
org_assembly = c("hg19",
"hg38",
"mm10",
"dre10",
"rn6",
"dm6",
"ce11",
"sc3"),
near = TRUE,
backG = '',
backGType = 'pc_gene',
isTADSearch = FALSE,
TAD = c(tad_hg19, tad_dmel, tad_hg38, tad_mm10),
express = FALSE,
isCustomExp = FALSE,
cancer,
exp1,
exp2,
label1 = '',
label2 = '',
isUnionCorGene = FALSE,
databaseFile) {
if (missing(region)) {
message("Bed file is missing. Please read any bed file is missing?")
}
if (missing(org_assembly)) {
message("Assembly version is missing?")
}
if (class(pkg.env$mart)[1] != "Mart") {
assembly(org_assembly)
}
if (near) {
ifelse(
pkg.env$searchRegion == 'all',
nearGene <-
getUCSC(
bedfile = region,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
ifelse(
pkg.env$searchRegion == 'exon',
nearGene <-
getNearToExon(
bedfile = region,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
nearGene <-
getNearToIntron(
bedfile = region,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
)
)
)
}
else{
nearGene <-
getUCSC(
bedfile = region,
upstream = 0,
downstream = 0,
org_assembly = org_assembly
)
}
if (isTADSearch) {
tadGene <-
getTADOverlap(
bedfile = geneLoc,
tad = TAD,
cellline = pkg.env$cellline,
org_assembly = org_assembly,
near = near,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream
)
if (near)
nearGene <-
as.data.frame(intersect(unlist(nearGene), unlist(tadGene)))
else
nearGene <- tadGene
}
if (express) {
if (!isCustomExp) {
nearG <-
corrbasedMrna(
mRNAgene = nearGene,
cancer = cancer,
minAbsCor = pkg.env$minAbsCor,
databaseFile = databaseFile
)
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$feature)
else
nearGene <- union(unlist(nearGene), nearG$feature)
}
else{
nearG <- calculateCorr(
exp1 = exp1,
exp2 = exp2,
label1 = label1 ,
label2 = label2,
corrMethod = pkg.env$corrMethod,
varCutoff = pkg.env$varCutoff,
corCutoff = pkg.env$minAbsCor,
pcut = pkg.env$pcut,
alternate = pkg.env$alternate,
conf = pkg.env$conf
)
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$SecondExp)
else
nearGene <- union(unlist(nearGene), nearG$SecondExp)
}
}
if (length(nearGene) == 0) {
message("No common gene is found")
methods::new(
"NoRCE",
ID = '',
Term = '',
geneList = list(),
pvalue = 0,
pAdj = 0,
GeneRatio = '',
BckRatio = ''
)
}
else{
enrichedGene <-
goEnrichment(
genes = nearGene,
GOtype = pkg.env$GOtype,
org_assembly = org_assembly,
pCut = pkg.env$pCut,
pAdjCut = pkg.env$pAdjCut,
backG = backG,
backGType = backGType,
enrichTest = pkg.env$enrichTest,
pAdjust = pkg.env$pAdjust,
min = pkg.env$min
)
return(enrichedGene)
}
}
#' Given gene regions that fall in the given upstream and downstream region
#' of mRNAs of interest, pathway enrichment analysis is carried out
#'
#' @param region Bed format of input gene regions other than miRNA. Input must
#' be Granges object.
#' @param org_assembly Genome assembly of interest for the analysis. Possible
#' assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat,
#' "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and
#' "hg38" for human
#' @param near Boolean value presents whether cis-neighbourhood should be
#' considered in the analysis
#' @param isTADSearch Boolean value that shows whether TAD analysis is
#' performed. This value has to be TRUE for TAD analysis.
#' @param TAD TAD genomic regions for the species. Predefined TAD regions or
#' any new TAD regions can be used for the analysis. TAD regions must be
#' formated as GRanges object. Predefined TAD regions are 'tad_hg19',
#' 'tad_hg38', 'tad_mm10', 'tad_dmel' for hg19, hg38, mm9 and dm6 assembly,
#' respectively.
#' @param gmtName Custom pathway gmt file
#' @param express Boolean variable whether co-expression analysis is
#' performed. If this option is set to TRUE, co-expression analysis will
#' be performed.
#' @param isCustomExp Boolean variable whether co-expression analysis with
#' custom data will be performed. When this option is set, exp1 and exp2
#' parameters must be defined.
#' @param cancer Defines the name of the TCGA project code such as 'BRCA' for
#' correlation analysis. Possible cancer types ACC, BLCA, BRCA, CESC,
#' CHOL, COAD, COADREAD, DLBC, ESCA, GBMLGG, HNSC, KICH, KIPAN, KIRC,
#' KIRP, LGG, LIHC, LUAD, LUSC, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM,
#' STAD, STES, TGCT, THCA, THYM, UCEC, UCS, UVM
#' @param exp1 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param exp2 Custom expression data matrix. Columns must be genes and rows
#' must be patients. If gene names are provided as header, no need to
#' redefine the headers(labels) of the expression data.
#' @param label1 Gene names of the custom exp1 expression data. If it is not
#' provided, column name of the exp1 data will be taken.
#' @param label2 Gene names of the custom exp2 expression data. If it is not
#' provided, column name of the exp2 data will be taken.
#' @param databaseFile Path of miRcancer.db file
#' @param isUnionCorGene Boolean value that shows whether union of the output
#' of the co-expression analysis and the other analysis should be
#' considered
#' @param isGeneEnrich Boolean value whether gene enrichment should be
#' performed
#'
#' @return Pathway enrichment object of the given input
#'
#' @examples
#'
#' regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")
#' regionNC <- rtracklayer::import(regions, format = "BED")
#' ncPath<-geneRegionPathwayEnricher(region = regionNC,
#' org_assembly = 'hg19',
#' near = TRUE)
#' @export
geneRegionPathwayEnricher <-
function(region,
org_assembly = c("hg19",
"hg38",
"mm10",
"dre10",
"rn6",
"dm6",
"ce11",
"sc3"),
near = FALSE,
isTADSearch = FALSE,
TAD = tad_hg19,
gmtName = '',
express = FALSE,
isCustomExp = FALSE,
cancer,
exp1,
exp2,
label1 = '',
label2 = '',
isUnionCorGene = FALSE,
databaseFile,
isGeneEnrich = FALSE) {
if (missing(region)) {
message("Bed file is missing. Please read any bed file is missing?")
}
if (missing(org_assembly)) {
message("Assembly version is missing?")
}
if (class(pkg.env$mart)[1] != "Mart") {
assembly(org_assembly)
}
if (near) {
ifelse(
pkg.env$searchRegion == 'all',
nearGene <-
getUCSC(
bedfile = region,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
ifelse(
pkg.env$searchRegion == 'exon',
nearGene <-
getNearToExon(
bedfile = region,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
),
nearGene <-
getNearToIntron(
bedfile = region,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream,
org_assembly = org_assembly
)
)
)
}
else{
nearGene <-
getUCSC(
bedfile = region,
upstream = 0,
downstream = 0,
org_assembly = org_assembly
)
}
if (isTADSearch) {
tadGene <-
getTADOverlap(
bedfile = geneLoc,
tad = TAD,
cellline = pkg.env$cellline,
org_assembly = org_assembly,
near = near,
upstream = pkg.env$upstream,
downstream = pkg.env$downstream
)
if (near)
nearGene <-
as.data.frame(intersect(unlist(nearGene), unlist(tadGene)))
else
nearGene <- tadGene
}
if (express) {
if (!isCustomExp) {
nearG <-
corrbasedMrna(
mRNAgene = nearGene,
cancer = cancer,
minAbsCor = pkg.env$minAbsCor,
databaseFile = databaseFile
)
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$feature)
else
nearGene <- union(unlist(nearGene), nearG$feature)
}
else{
nearG <- calculateCorr(
exp1 = exp1,
exp2 = exp2,
label1 = label1 ,
label2 = label2,
corrMethod = pkg.env$corrMethod,
varCutoff = pkg.env$varCutoff,
corCutoff = pkg.env$minAbsCor,
pcut = pkg.env$pcut,
alternate = pkg.env$alternate,
conf = pkg.env$conf
)
if (!isUnionCorGene)
nearGene <- intersect(unlist(nearGene), nearG$SecondExp)
else
nearGene <- union(unlist(nearGene), nearG$SecondExp)
}
}
if (length(nearGene) == 0) {
message("No common gene is found")
methods::new(
"NoRCE",
ID = '',
Term = '',
geneList = list(),
pvalue = 0,
pAdj = 0,
GeneRatio = '',
BckRatio = ''
)
}
else{
ifelse(
pkg.env$pathwayType == 'kegg',
pth <- 1,
ifelse(
pkg.env$pathwayType == 'reactome',
pth <- 2,
ifelse(pkg.env$pathwayType == 'wiki',
pth <- 3,
pth <- 4)
)
)
funclist <- list(KeggEnrichment,
reactomeEnrichment,
WikiEnrichment,
pathwayEnrichment)
enrichedGene <- funclist[[pth]](
genes = nearGene,
gmtFile = gmtName,
org_assembly = org_assembly,
pCut = pkg.env$pCut,
pAdjCut = pkg.env$pAdjCut,
pAdjust = pkg.env$pAdjust,
isSymbol = pkg.env$isSymbol,
min = pkg.env$min,
isGeneEnrich = isGeneEnrich
)
return(enrichedGene)
}
}
