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update

guldenolgun authored on 14/01/2020 16:56:30
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@@ -5,11 +5,17 @@
5 5
 \title{For a given gmt file of a specific pathway database, pathway enrichment
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 can be performed. Function supports Entrez ID and symbol based gmt file.}
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 \usage{
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-pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",
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-  "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), pCut = 0.05,
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-  pAdjCut = 0.05, pAdjust = c("holm", "hochberg", "hommel",
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-  "bonferroni", "BH", "BY", "fdr", "none"), isSymbol, min = 5,
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-  isGeneEnrich = FALSE)
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+pathwayEnrichment(
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+  genes,
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+  gmtFile,
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+  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"),
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+  pCut = 0.05,
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+  pAdjCut = 0.05,
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+  pAdjust = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"),
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+  isSymbol,
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+  min = 5,
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+  isGeneEnrich = FALSE
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+)
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 }
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 \arguments{
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 \item{genes}{Input genes}
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@@ -46,12 +52,3 @@ Pathway Enrichment
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 For a given gmt file of a specific pathway database, pathway enrichment
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 can be performed. Function supports Entrez ID and symbol based gmt file.
48 54
 }
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-\examples{
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-
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-wp.gmt <-rWikiPathways::downloadPathwayArchive(
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-                         organism = "Homo sapiens",format = "gmt")
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-a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt,
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-                       org_assembly = 'hg19',isGeneEnrich = FALSE,
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-                       isSymbol = FALSE)
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-
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-}
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update

guldenolgun authored on 05/11/2019 17:09:21
Showing1 changed files
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@@ -2,8 +2,8 @@
2 2
 % Please edit documentation in R/pathway.R
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 \name{pathwayEnrichment}
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 \alias{pathwayEnrichment}
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-\title{For a given gmt file of a specific pathway database, pathway enrichment can
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-be performed. Function supports Entrez ID and symbol based gmt file.}
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+\title{For a given gmt file of a specific pathway database, pathway enrichment
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+can be performed. Function supports Entrez ID and symbol based gmt file.}
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 \usage{
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 pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",
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   "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), pCut = 0.05,
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@@ -43,8 +43,8 @@ performed}
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 Pathway Enrichment
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 }
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 \description{
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-For a given gmt file of a specific pathway database, pathway enrichment can
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-be performed. Function supports Entrez ID and symbol based gmt file.
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+For a given gmt file of a specific pathway database, pathway enrichment
47
+can be performed. Function supports Entrez ID and symbol based gmt file.
48 48
 }
49 49
 \examples{
50 50
 
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update

guldenolgun authored on 24/10/2019 21:12:53
Showing1 changed files
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@@ -50,8 +50,8 @@ be performed. Function supports Entrez ID and symbol based gmt file.
50 50
 
51 51
 wp.gmt <-rWikiPathways::downloadPathwayArchive(
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                          organism = "Homo sapiens",format = "gmt")
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-a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt, 
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-                       org_assembly = 'hg19',isGeneEnrich = FALSE, 
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-                       isSymbol = FALSE)                   
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+a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt,
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+                       org_assembly = 'hg19',isGeneEnrich = FALSE,
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+                       isSymbol = FALSE)
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57 57
 }
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update

guldenolgun authored on 20/10/2019 12:04:41
Showing1 changed files
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@@ -46,3 +46,12 @@ Pathway Enrichment
46 46
 For a given gmt file of a specific pathway database, pathway enrichment can
47 47
 be performed. Function supports Entrez ID and symbol based gmt file.
48 48
 }
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+\examples{
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+
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+wp.gmt <-rWikiPathways::downloadPathwayArchive(
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+                         organism = "Homo sapiens",format = "gmt")
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+a <- pathwayEnrichment(genes = breastmRNA[1:100,], gmtFile = wp.gmt, 
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+                       org_assembly = 'hg19',isGeneEnrich = FALSE, 
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+                       isSymbol = FALSE)                   
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+
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+}
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update

guldenolgun authored on 24/08/2019 09:32:35
Showing1 changed files
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@@ -2,7 +2,7 @@
2 2
 % Please edit documentation in R/pathway.R
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 \name{pathwayEnrichment}
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 \alias{pathwayEnrichment}
5
-\title{For a given gmt file of a specific pathway database, pathway enrichment can 
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+\title{For a given gmt file of a specific pathway database, pathway enrichment can
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 be performed. Function supports Entrez ID and symbol based gmt file.}
7 7
 \usage{
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 pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",
... ...
@@ -16,33 +16,33 @@ pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",
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17 17
 \item{gmtFile}{File path of the gmt file}
18 18
 
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-\item{org_assembly}{Genome assembly of interest for the analysis. Possible 
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-assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, 
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-"dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and 
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+\item{org_assembly}{Genome assembly of interest for the analysis. Possible
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+assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat,
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+"dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and
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 "hg38" for human}
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24 24
 \item{pCut}{Threshold value for the pvalue. Default value is 0.05}
25 25
 
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-\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given 
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+\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given
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 method. Default value is 0.05.}
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-\item{pAdjust}{Methods of the adjusted p-values. Possible methods are 
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+\item{pAdjust}{Methods of the adjusted p-values. Possible methods are
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 "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none"}
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 \item{isSymbol}{Boolean value that controls the gene formats. If it is TRUE,
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-gene format of the gmt file should be symbol. Otherwise, gene format 
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+gene format of the gmt file should be symbol. Otherwise, gene format
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 must be ENTREZ ID.}
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-\item{min}{Minimum number of genes that are required for enrichment. By 
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+\item{min}{Minimum number of genes that are required for enrichment. By
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 default, it is set to 5.}
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-\item{isGeneEnrich}{Boolean value whether gene enrichment should be 
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+\item{isGeneEnrich}{Boolean value whether gene enrichment should be
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 performed}
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 }
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 \value{
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 Pathway Enrichment
44 44
 }
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 \description{
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-For a given gmt file of a specific pathway database, pathway enrichment can 
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+For a given gmt file of a specific pathway database, pathway enrichment can
47 47
 be performed. Function supports Entrez ID and symbol based gmt file.
48 48
 }
Browse code

update

guldenolgun authored on 23/08/2019 19:59:51
Showing1 changed files
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@@ -2,40 +2,47 @@
2 2
 % Please edit documentation in R/pathway.R
3 3
 \name{pathwayEnrichment}
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 \alias{pathwayEnrichment}
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-\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.}
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+\title{For a given gmt file of a specific pathway database, pathway enrichment can 
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+be performed. Function supports Entrez ID and symbol based gmt file.}
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 \usage{
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-pathwayEnrichment(genes, gmtFile, hg, pCut = 0.05, pAdjCut = 0.05,
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-  pAdjust = "BH", isSymbol, min = 5, isGeneEnrich = FALSE)
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+pathwayEnrichment(genes, gmtFile, org_assembly = c("hg19", "hg38",
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+  "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), pCut = 0.05,
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+  pAdjCut = 0.05, pAdjust = c("holm", "hochberg", "hommel",
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+  "bonferroni", "BH", "BY", "fdr", "none"), isSymbol, min = 5,
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+  isGeneEnrich = FALSE)
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 }
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 \arguments{
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 \item{genes}{Input genes}
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 \item{gmtFile}{File path of the gmt file}
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-\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}
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+\item{org_assembly}{Genome assembly of interest for the analysis. Possible 
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+assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, 
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+"dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and 
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+"hg38" for human}
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17 24
 \item{pCut}{Threshold value for the pvalue. Default value is 0.05}
18 25
 
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-\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given method. Default value is 0.05.}
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+\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given 
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+method. Default value is 0.05.}
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-\item{pAdjust}{Methods of the adjusted p-values. Possible methods are "bonferroni", "holm", "BH"(default)}
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+\item{pAdjust}{Methods of the adjusted p-values. Possible methods are 
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+"holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none"}
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-\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.}
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+\item{isSymbol}{Boolean value that controls the gene formats. If it is TRUE,
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+gene format of the gmt file should be symbol. Otherwise, gene format 
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+must be ENTREZ ID.}
24 35
 
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-\item{min}{Minimum number of genes that are required for enrichment. By default, it is set to 5.}
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+\item{min}{Minimum number of genes that are required for enrichment. By 
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+default, it is set to 5.}
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-\item{isGeneEnrich}{Boolean value whether gene enrichment should be performed}
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+\item{isGeneEnrich}{Boolean value whether gene enrichment should be 
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+performed}
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 }
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 \value{
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 Pathway Enrichment
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 }
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 \description{
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-For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.
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-}
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-\examples{
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-tmpGene <- breastmRNA[1:100,]
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-\dontrun{
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-br_enr<-pathwayEnrichment(genes = tmpGene,hg='hg19',
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-    gmtFile = 'Human_AllPathways_February_01_2019_symbol.gmt',isSymbol = TRUE)
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-}
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+For a given gmt file of a specific pathway database, pathway enrichment can 
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+be performed. Function supports Entrez ID and symbol based gmt file.
41 48
 }
Browse code

First Version

guldenolgun authored on 26/05/2019 12:07:28
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,41 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/pathway.R
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+\name{pathwayEnrichment}
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+\alias{pathwayEnrichment}
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+\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.}
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+\usage{
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+pathwayEnrichment(genes, gmtFile, hg, pCut = 0.05, pAdjCut = 0.05,
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+  pAdjust = "BH", isSymbol, min = 5, isGeneEnrich = FALSE)
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+}
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+\arguments{
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+\item{genes}{Input genes}
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+
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+\item{gmtFile}{File path of the gmt file}
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+
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+\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}
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+
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+\item{pCut}{Threshold value for the pvalue. Default value is 0.05}
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+
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+\item{pAdjCut}{Cutoff value for the adjusted p-values using one of given method. Default value is 0.05.}
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+
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+\item{pAdjust}{Methods of the adjusted p-values. Possible methods are "bonferroni", "holm", "BH"(default)}
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+
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+\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.}
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+
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+\item{min}{Minimum number of genes that are required for enrichment. By default, it is set to 5.}
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+
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+\item{isGeneEnrich}{Boolean value whether gene enrichment should be performed}
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+}
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+\value{
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+Pathway Enrichment
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+}
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+\description{
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+For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.
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+}
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+\examples{
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+tmpGene <- breastmRNA[1:100,]
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+\dontrun{
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+br_enr<-pathwayEnrichment(genes = tmpGene,hg='hg19',
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+    gmtFile = 'Human_AllPathways_February_01_2019_symbol.gmt',isSymbol = TRUE)
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+}
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+}