@@ -5,11 +5,17 @@

 \title{For a given gmt file of a specific pathway database, pathway enrichment

 can be performed. Function supports Entrez ID and symbol based gmt file.}

 \usage{

-pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",

-  "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), pCut = 0.05,

-  pAdjCut = 0.05, pAdjust = c("holm", "hochberg", "hommel",

-  "bonferroni", "BH", "BY", "fdr", "none"), isSymbol, min = 5,

-  isGeneEnrich = FALSE)

+pathwayEnrichment(

+  genes,

+  gmtFile,

+  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"),

+  pCut = 0.05,

+  pAdjCut = 0.05,

+  pAdjust = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"),

+  isSymbol,

+  min = 5,

+  isGeneEnrich = FALSE

+)

 }

 \arguments{

 \item{genes}{Input genes}

@@ -46,12 +52,3 @@ Pathway Enrichment

 For a given gmt file of a specific pathway database, pathway enrichment

 can be performed. Function supports Entrez ID and symbol based gmt file.

 }

-\examples{

-

-wp.gmt <-rWikiPathways::downloadPathwayArchive(

-                         organism = "Homo sapiens",format = "gmt")

-a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt,

-                       org_assembly = 'hg19',isGeneEnrich = FALSE,

-                       isSymbol = FALSE)

-

-}

@@ -2,8 +2,8 @@

 % Please edit documentation in R/pathway.R

 \name{pathwayEnrichment}

 \alias{pathwayEnrichment}

-\title{For a given gmt file of a specific pathway database, pathway enrichment can

-be performed. Function supports Entrez ID and symbol based gmt file.}

+\title{For a given gmt file of a specific pathway database, pathway enrichment

+can be performed. Function supports Entrez ID and symbol based gmt file.}

 \usage{

 pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",

   "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), pCut = 0.05,

@@ -43,8 +43,8 @@ performed}

 Pathway Enrichment

 }

 \description{

-For a given gmt file of a specific pathway database, pathway enrichment can

-be performed. Function supports Entrez ID and symbol based gmt file.

+For a given gmt file of a specific pathway database, pathway enrichment

+can be performed. Function supports Entrez ID and symbol based gmt file.

 }

 \examples{

@@ -50,8 +50,8 @@ be performed. Function supports Entrez ID and symbol based gmt file.

 wp.gmt <-rWikiPathways::downloadPathwayArchive(

                          organism = "Homo sapiens",format = "gmt")

-a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt, 

-                       org_assembly = 'hg19',isGeneEnrich = FALSE, 

-                       isSymbol = FALSE)                   

+a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt,

+                       org_assembly = 'hg19',isGeneEnrich = FALSE,

+                       isSymbol = FALSE)

 }

@@ -46,3 +46,12 @@ Pathway Enrichment

 For a given gmt file of a specific pathway database, pathway enrichment can

 be performed. Function supports Entrez ID and symbol based gmt file.

 }

+\examples{

+

+wp.gmt <-rWikiPathways::downloadPathwayArchive(

+                         organism = "Homo sapiens",format = "gmt")

+a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt, 

+                       org_assembly = 'hg19',isGeneEnrich = FALSE, 

+                       isSymbol = FALSE)                   

+

+}

@@ -2,7 +2,7 @@

 % Please edit documentation in R/pathway.R

 \name{pathwayEnrichment}

 \alias{pathwayEnrichment}

-\title{For a given gmt file of a specific pathway database, pathway enrichment can 

+\title{For a given gmt file of a specific pathway database, pathway enrichment can

 be performed. Function supports Entrez ID and symbol based gmt file.}

 \usage{

 pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",

@@ -16,33 +16,33 @@ pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",

 \item{gmtFile}{File path of the gmt file}

-\item{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 

+\item{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}

 \item{pCut}{Threshold value for the pvalue. Default value is 0.05}

-\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given 

+\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given

 method. Default value is 0.05.}

-\item{pAdjust}{Methods of the adjusted p-values. Possible methods are 

+\item{pAdjust}{Methods of the adjusted p-values. Possible methods are

 "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none"}

 \item{isSymbol}{Boolean value that controls the gene formats. If it is TRUE,

-gene format of the gmt file should be symbol. Otherwise, gene format 

+gene format of the gmt file should be symbol. Otherwise, gene format

 must be ENTREZ ID.}

-\item{min}{Minimum number of genes that are required for enrichment. By 

+\item{min}{Minimum number of genes that are required for enrichment. By

 default, it is set to 5.}

-\item{isGeneEnrich}{Boolean value whether gene enrichment should be 

+\item{isGeneEnrich}{Boolean value whether gene enrichment should be

 performed}

 }

 \value{

 Pathway Enrichment

 }

 \description{

-For a given gmt file of a specific pathway database, pathway enrichment can 

+For a given gmt file of a specific pathway database, pathway enrichment can

 be performed. Function supports Entrez ID and symbol based gmt file.

 }

@@ -2,40 +2,47 @@

 % Please edit documentation in R/pathway.R

 \name{pathwayEnrichment}

 \alias{pathwayEnrichment}

-\title{For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.}

+\title{For a given gmt file of a specific pathway database, pathway enrichment can 

+be performed. Function supports Entrez ID and symbol based gmt file.}

 \usage{

-pathwayEnrichment(genes, gmtFile, hg, pCut = 0.05, pAdjCut = 0.05,

-  pAdjust = "BH", isSymbol, min = 5, isGeneEnrich = FALSE)

+pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",

+  "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), pCut = 0.05,

+  pAdjCut = 0.05, pAdjust = c("holm", "hochberg", "hommel",

+  "bonferroni", "BH", "BY", "fdr", "none"), isSymbol, min = 5,

+  isGeneEnrich = FALSE)

 }

 \arguments{

 \item{genes}{Input genes}

 \item{gmtFile}{File path of the gmt file}

-\item{hg}{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}

+\item{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}

 \item{pCut}{Threshold value for the pvalue. Default value is 0.05}

-\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given method. Default value is 0.05.}

+\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given 

+method. Default value is 0.05.}

-\item{pAdjust}{Methods of the adjusted p-values. Possible methods are "bonferroni", "holm", "BH"(default)}

+\item{pAdjust}{Methods of the adjusted p-values. Possible methods are 

+"holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none"}

-\item{isSymbol}{Boolean value that controls the gene formats. If it is TRUE, gene format of the gmt file should be symbol. Otherwise, gene format must be ENTREZ ID.}

+\item{isSymbol}{Boolean value that controls the gene formats. If it is TRUE,

+gene format of the gmt file should be symbol. Otherwise, gene format 

+must be ENTREZ ID.}

-\item{min}{Minimum number of genes that are required for enrichment. By default, it is set to 5.}

+\item{min}{Minimum number of genes that are required for enrichment. By 

+default, it is set to 5.}

-\item{isGeneEnrich}{Boolean value whether gene enrichment should be performed}

+\item{isGeneEnrich}{Boolean value whether gene enrichment should be 

+performed}

 }

 \value{

 Pathway Enrichment

 }

 \description{

-For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.

-}

-\examples{

-tmpGene <- breastmRNA[1:100,]

-\dontrun{

-br_enr<-pathwayEnrichment(genes = tmpGene,hg='hg19',

-    gmtFile = 'Human_AllPathways_February_01_2019_symbol.gmt',isSymbol = TRUE)

-}

+For a given gmt file of a specific pathway database, pathway enrichment can 

+be performed. Function supports Entrez ID and symbol based gmt file.

 }

new file mode 100644

@@ -0,0 +1,41 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/pathway.R

+\name{pathwayEnrichment}

+\alias{pathwayEnrichment}

+\title{For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.}

+\usage{

+pathwayEnrichment(genes, gmtFile, hg, pCut = 0.05, pAdjCut = 0.05,

+  pAdjust = "BH", isSymbol, min = 5, isGeneEnrich = FALSE)

+}

+\arguments{

+\item{genes}{Input genes}

+

+\item{gmtFile}{File path of the gmt file}

+

+\item{hg}{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}

+

+\item{pCut}{Threshold value for the pvalue. Default value is 0.05}

+

+\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given method. Default value is 0.05.}

+

+\item{pAdjust}{Methods of the adjusted p-values. Possible methods are "bonferroni", "holm", "BH"(default)}

+

+\item{isSymbol}{Boolean value that controls the gene formats. If it is TRUE, gene format of the gmt file should be symbol. Otherwise, gene format must be ENTREZ ID.}

+

+\item{min}{Minimum number of genes that are required for enrichment. By default, it is set to 5.}

+

+\item{isGeneEnrich}{Boolean value whether gene enrichment should be performed}

+}

+\value{

+Pathway Enrichment

+}

+\description{

+For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.

+}

+\examples{

+tmpGene <- breastmRNA[1:100,]

+\dontrun{

+br_enr<-pathwayEnrichment(genes = tmpGene,hg='hg19',

+    gmtFile = 'Human_AllPathways_February_01_2019_symbol.gmt',isSymbol = TRUE)

+}

+}