Pourya Naderi authored on 07/01/2022 03:27:44 | ... | ... |
@@ -4,7 +4,13 @@ |
| 4 | 4 |
\alias{pathwayGeneTab}
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| 5 | 5 |
\title{Pathway-Gene Associations}
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| 6 | 6 |
\usage{
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-pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA) |
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+pathwayGeneTab( |
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+ pathAdress = NA, |
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+ pathwayList = NA, |
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+ fromType = "ENTREZID", |
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+ toType = "ENSEMBL", |
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+ outDir = NA |
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+) |
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| 8 | 14 |
} |
| 9 | 15 |
\arguments{
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\item{pathAdress}{Address to an RDS file containing list of pathways where
|
| ... | ... |
@@ -13,6 +19,10 @@ each element is a list of genes similar to GMT format.} |
| 13 | 19 |
\item{pathwayList}{If you wish to use a list of pathways instead of a file
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| 14 | 20 |
use this argument instead. The list must contain no NA values.} |
| 15 | 21 |
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+\item{fromType}{gene annotation type used in your input data.}
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+ |
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+\item{toType}{gene annotation type to be produced in the output.}
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+ |
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| 16 | 26 |
\item{outDir}{Address to save an RDS for a table of pathway-gene association}
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| 17 | 27 |
} |
| 18 | 28 |
\value{
|
Pourya Naderi authored on 01/12/2021 20:24:29 | ... | ... |
@@ -21,3 +21,12 @@ pathExpTab Table of pathway-gene association. |
| 21 | 21 |
\description{
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| 22 | 22 |
Generates a table of pathways and genes associations. |
| 23 | 23 |
} |
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+\examples{
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+pathway1 <- c("125", "3099", "126")
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+pathway2 <- c("5232", "5230", "5162")
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+pathList <- list("Path1" = pathway1, "Path2" = pathway2)
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+res <- pathwayGeneTab(pathwayList = pathList) |
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+ |
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+data(msigdb_c2) |
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+pathwayGeneTab(pathwayList = msigdb_c2[1:2]) |
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+} |
Pourya Naderi authored on 01/12/2021 15:17:16 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,23 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/utils.R |
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+\name{pathwayGeneTab}
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+\alias{pathwayGeneTab}
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+\title{Pathway-Gene Associations}
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+\usage{
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+pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA) |
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+} |
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+\arguments{
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+\item{pathAdress}{Address to an RDS file containing list of pathways where
|
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+each element is a list of genes similar to GMT format.} |
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+ |
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+\item{pathwayList}{If you wish to use a list of pathways instead of a file
|
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+use this argument instead. The list must contain no NA values.} |
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+ |
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+\item{outDir}{Address to save an RDS for a table of pathway-gene association}
|
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+} |
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+\value{
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+pathExpTab Table of pathway-gene association. |
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+} |
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+\description{
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+Generates a table of pathways and genes associations. |
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+} |
Pourya Naderi authored on 01/12/2021 15:16:55 | 1 | 1 |
deleted file mode 100644 |
| ... | ... |
@@ -1,23 +0,0 @@ |
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-% Generated by roxygen2: do not edit by hand |
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-% Please edit documentation in R/utils.R |
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-\name{pathwayGeneTab}
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-\alias{pathwayGeneTab}
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-\title{Pathway-Gene Associations}
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-\usage{
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-pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA) |
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-} |
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-\arguments{
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-\item{pathAdress}{Address to an RDS file containing list of pathways where
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-each element is a list of genes similar to GMT format.} |
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- |
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-\item{pathwayList}{If you wish to use a list of pathways instead of a file
|
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-use this argument instead. The list must contain no NA values.} |
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- |
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-\item{outDir}{Address to save an RDS for a table of pathway-gene association}
|
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-} |
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-\value{
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-pathExpTab Table of pathway-gene association. |
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-} |
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-\description{
|
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-Generates a table of pathways and genes associations. |
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-} |
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Pourya Naderi authored on 18/11/2021 17:33:22 | ... | ... |
@@ -4,16 +4,16 @@ |
| 4 | 4 |
\alias{pathwayGeneTab}
|
| 5 | 5 |
\title{Pathway-Gene Associations}
|
| 6 | 6 |
\usage{
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-pathwayGeneTab(path.address = NA, pathway.list = NA, out.dir = NA) |
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+pathwayGeneTab(pathAdress = NA, pathwayList = NA, outDir = NA) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
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-\item{path.address}{Address to an RDS file containing list of pathways where
|
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+\item{pathAdress}{Address to an RDS file containing list of pathways where
|
|
| 11 | 11 |
each element is a list of genes similar to GMT format.} |
| 12 | 12 |
|
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-\item{pathway.list}{If you wish to use a list of pathways instead of a file
|
|
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+\item{pathwayList}{If you wish to use a list of pathways instead of a file
|
|
| 14 | 14 |
use this argument instead. The list must contain no NA values.} |
| 15 | 15 |
|
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-\item{out.dir}{Address to save an RDS for a table of pathway-gene association}
|
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+\item{outDir}{Address to save an RDS for a table of pathway-gene association}
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|
| 17 | 17 |
} |
| 18 | 18 |
\value{
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| 19 | 19 |
pathExpTab Table of pathway-gene association. |
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Pourya Naderi authored on 18/11/2021 16:00:50 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,23 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/utils.R |
|
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+\name{pathwayGeneTab}
|
|
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+\alias{pathwayGeneTab}
|
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+\title{Pathway-Gene Associations}
|
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+\usage{
|
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+pathwayGeneTab(path.address = NA, pathway.list = NA, out.dir = NA) |
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+} |
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+\arguments{
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+\item{path.address}{Address to an RDS file containing list of pathways where
|
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+each element is a list of genes similar to GMT format.} |
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+ |
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+\item{pathway.list}{If you wish to use a list of pathways instead of a file
|
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+use this argument instead. The list must contain no NA values.} |
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+ |
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+\item{out.dir}{Address to save an RDS for a table of pathway-gene association}
|
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+} |
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+\value{
|
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+pathExpTab Table of pathway-gene association. |
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+} |
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+\description{
|
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+Generates a table of pathways and genes associations. |
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+} |